Assays and methods of treatment relating to vitamin D insufficiency

ABSTRACT

Described herein are assays directed to determining the level of bioavailable or free vitamin D in a blood sample in a subject. The values determined for bioavailable or free vitamin D indicate whether the subject suffers from insufficient levels of vitamin D. Also described herein are methods of treatment for vitamin D insufficiency.

CLAIM OF PRIORITY

This application is a U.S. National Phase Application under 35 U.S.C. §371 of International Patent Application No. PCT/US2014/036650, filed on May 2, 2014, which claims the benefit of U.S. Provisional Patent Application Ser. No. 61/819,235, filed on May 3, 2013, and U.S. patent application Ser. No. 13/918,563, filed on Jun. 14, 2013 now U.S. Pat. No. 9,052,308, which claims the benefit of U.S. Patent Application No. 61/819,235, filed on May 3, 2013, and is a continuation in part of PCT/US2012/020407, filed on Jan. 6, 2012, which claims the benefit of U.S. Patent Application No. 61/430,643, filed on Jan. 7, 2011. The entire contents of the foregoing are hereby incorporated by reference.

GOVERNMENT SUPPORT

This invention was made with federal government support under Grant Number M01-(RR-01066)-Harvard Clinical and Translational Science Center awarded by the National Center for Research Resources and Grant Nos. K23 1K23DK081677 and R01 DK 094486 awarded by the National Institutes of Health. The U.S. Government has certain rights in the invention.

FIELD OF THE INVENTION

The invention is directed to assays and methods of treatment relating to vitamin D insufficiency.

BACKGROUND OF THE INVENTION

Vitamin D insufficiency (variously defined as <20 to 30 ng/mL of total serum 25(OH)D as currently measured) is highly prevalent, even in otherwise healthy individuals. Reported in >1 billion people worldwide, it is now recognized as one of the most common subclinical medical conditions in the world. Beyond rickets, a manifestation of severe vitamin D insufficiency recognized since the 17th century,³⁵ vitamin D deficiency (commonly defined as <10-25 ng/mL of total serum 25[OH]D)^(21,34,36) has since been associated with an increased risk of osteoporosis, cancer, infectious disease, CVD disease, allergy, asthma, multiple sclerosis, muscle weakness, rheumatoid arthritis, and diabetes. Low vitamin D can arise from insufficient intake from nutritional sources, insufficient synthesis (via UV-B radiation of the skin), adiposity, age, physical activity, or other disease-related factors such as diabetes, bariatric surgery, fat malabsorption syndromes, and kidney disease.^(14,37,38) The use of sunscreen with sun protection factor (SPF)≧30 reduces the ability of the skin to produce vitamin D by 99%, thus contributing to the pandemic.

One recent study found that vitamin D insufficiency was present in 72% of community-dwelling men older than 65 years of age, and in up to 86% of those men who were obese, lived at higher latitudes, or infrequently participated in outdoor activities.¹⁷ Although vitamin D deficiency is less common, it is estimated to affect 26%-54% of community-dwelling older adults and 57% of hospitalized patients.^(17,36,40) A recognized problem in older adults, people of all ages who live in diverse geographic locations are also susceptible, including sunny climate dwellers.⁴¹ A study of younger adults with limited exposure to the outdoors in a northeastern urban setting reported that 32% of students and doctors aged 18-29 years were vitamin D deficient at the end of the winter.⁴² In diseases including diabetes, rheumatoid arthritis, renal disease, as well as in individuals who are obese, hospitalized, pregnant, newborn, highly deficient levels of this hormone are common.^(40,43-45) Current recommendations for vitamin D supplementation are largely inadequate.^(17,46,47) According to Holick,⁴⁶ 25(OH)D is the most-ordered hormone assay in the US, used as the basis for treatment recommendations. However, assay results as well as cutoff levels of 25(OH)D to define the extent of vitamin D insufficiency are subject to considerable variation. Given the prevalence and breadth of illnesses potentially associated with low vitamin D, gaining a better understanding of vitamin D status to guide management of vitamin D insufficiency is a public health priority. The Institute of Medicine (IOM) has recognized that that assay variation and lack of consensus regarding cutoffs defining insufficiency/deficiency have caused confusion about the appropriate dietary intake of vitamin D.³³ The IOM has also cautioned against excessive intake due to the risks of kidney and tissue damage and have urged more targeted research in this area. Importantly, the method used to determine vitamin D status should be clinically relevant and applicable across diverse populations.

SUMMARY OF INVENTION

Described herein are methods, assays, methods of treatment, and systems related to determining the level of free and/or bioavailable vitamin D in a blood sample obtained from a subject.

In one aspect, the invention relates to an assay comprising a) analyzing a blood sample obtained from a subject to determine a level of VDBP (vitamin D binding protein) polypeptide, albumin polypeptide and total vitamin D; wherein a level of bioavailable vitamin D is: =(K _(alb)*[Alb]+1)*[Free Vitamin D] and wherein a level of free vitamin D is: ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K _(DBP)}).

In some embodiments, a level of bioavailable vitamin D lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable vitamin D in a population of healthy subjects can indicate that the subject has a vitamin D insufficiency. In some embodiments, the vitamin D can be selected from the group consisting of:

25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.

In another aspect, the invention features methods for determining a Vitamin D Index for a subject. The methods include determining total 25(OH)D concentration in the subject; determining a VDBP concentration in the subject; and calculating (e.g., using a processor as known in the art and described herein) a ratio of total 25(OH)D concentrations divided by VDBP concentrations, thereby determining the Vitamin D Index for the subject.

In some embodiments, % bioavailable radioligand (defined by the ratio of adsorbed radioligand divided by total radioligand) is converted into calculated % bioavailable 25(OH)D, e.g., using a calibrator standard curves (e.g., as in FIG. 12). The concentration of bioavailable 25(OH)D (in ng/ml) in a patient sample is then obtained by multiplying their measured total 25(OH)D concentrations by the calculated % bioavailable 25(OH)D.

In some embodiments, the methods include determining a VDBP genotype in the subject; and comparing the Vitamin D Index to a reference Index for the subject's genotype; wherein the presence of a Vitamin D Index below the reference Index indicates that the subject has a vitamin D insufficiency.

In some embodiments, determining the level of VDBP polypeptide or albumin polypeptide can comprise the use of a method selected from the group consisting of: enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; immunoturbidimetric assay; immunonephelometric assay; dye-based photometric assay; western blot; immunoprecipitation; radioimmunological assay (RIA); radioimmunometric assay; immunofluorescence assay and mass spectroscopy.

In some embodiments, determining the level of total vitamin D can comprise the use of a method selected from the group consisting of: radioimmunoassay; liquid chromatography tandem mass spectroscopy; enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; and high-pressure liquid chromatography.

In some embodiments, an insufficiency of vitamin D can indicate an increased risk of a condition selected from the group consisting of: decreased bone density; decreased bone mineral density; bone fractures; bone resorption; rickets; osteitis fibrosa cystica; fibrogenesis imperfect ossium; osteosclerosis; osteoporosis; osteomalacia; elevated parathyroid hormone levels; parathyroid gland hyperplasia; secondary hyperparathyroidism; hypocalcemia; infection; cancer; psoriasis; cardiovascular disease; renal osteodystrophy; renal disease; end-stage renal disease; chronic kidney disease; chronic kidney disease-associated mineral and bone disorder; extraskeletal calcification; obesity; allergy, asthama; multiple sclerosis; muscle weakness; rheumatoid arthritis and diabetes.

In some embodiments, the invention can further comprise the step of administering a vitamin D insufficiency treatment to a subject who is determined to have a vitamin D insufficiency. In some embodiments, the treatment can comprise administering a compound selected from the group consisting of: calcitriol; dihydrotachysterol; doxercalciferol; paricalcitol; cholecalciferol and ergocalciferol.

In another aspect, the invention relates to an assay comprising; analyzing a blood sample obtained from a subject to determine a level of VDBP polypeptide, albumin polypeptide and total vitamin D; wherein a level of free vitamin D is: ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K _(DBP)}).

In some embodiments, a level of free vitamin D lower than a threshold level, e.g., the 25^(th) percentile value or 25% of the mean value, of free vitamin D in a population of healthy subjects can indicate that the subject has a vitamin D insufficiency. In some embodiments, the vitamin D can be selected from the group consisting of: 25-hydroxyvitamin D and 125-dihydroxyvitamin D.

In some embodiments, determining the level of VDBP polypeptide or albumin polypeptide can comprise the use of a method selected from the group consisting of: enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; immunoturbidimetric assay; immunonephelometric assay; dye-based photometric assay; western blot; immunoprecipitation; radioimmunological assay (RIA); radioimmunometric assay; immunofluorescence assay and mass spectroscopy.

In some embodiments, determining the level of total vitamin D can comprise the use of a method selected from the group consisting of: radioimmunoassay; liquid chromatography tandem mass spectroscopy; enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; and high-pressure liquid chromatography.

In some embodiments, an insufficiency of vitamin D can indicate an increased risk of a condition selected from the group consisting of: decreased bone density; decreased bone mineral density; bone fractures; bone resorption; rickets; osteitis fibrosa cystica fibrogenesis imperfect ossium; osteosclerosis; osteoporosis; osteomalacia; elevated parathyroid hormone levels; parathyroid gland hyperplasia; secondary hyperparathyroidism; hypocalcemia; infection; cancer; psoriasis; cardiovascular disease; renal osteodystrophy; renal disease; end-stage renal disease; chronic kidney disease; chronic kidney disease-associated mineral and bone disorder; extraskeletal calcification; obesity; allergy, asthama; multiple sclerosis; muscle weakness; rheumatoid arthritis and diabetes.

In some embodiments, the invention can further comprise the step of administering a vitamin D insufficiency treatment to a subject who is determined to have a vitamin D insufficiency. In some embodiments, the treatment can comprise administering a compound selected from the group consisting of: calcitriol; dihydrotachysterol; doxercalciferol; paricalcitol; cholecalciferol and ergocalciferol.

In another aspect, the invention relates to a method for treating a vitamin D insufficiency in a subject comprising detecting a level of VDBP polypeptide, albumin polypeptide and total vitamin D in a blood sample obtained from a subject; wherein a level of bioavailable vitamin D is: =(K _(alb)*[Alb]+1)*[Free Vitamin D] and wherein a level of free vitamin D is: ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K _(DBP)}). and administering a treatment for vitamin D insufficiency to the subject if the level of bioavailable vitamin D is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable vitamin D in a population of healthy subjects.

In some embodiments, the vitamin D can be selected from the group consisting of: 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.

In some embodiments, determining the level of VDBP polypeptide or albumin polypeptide can comprise the use of a method selected from the group consisting of: enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; immunoturbidimetric assay; immunonephelometric assay; dye-based photometric assay; western blot; immunoprecipitation; radioimmunological assay (RIA); radioimmunometric assay; immunofluorescence assay and mass spectroscopy.

In some embodiments, determining the level of total vitamin D can comprise the use of a method selected from the group consisting of: radioimmunoassay; liquid chromatography tandem mass spectroscopy; enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; and high-pressure liquid chromatography.

In some embodiments, an insufficiency of vitamin D can indicate an increased risk of a condition selected from the group consisting of: decreased bone density; decreased bone mineral density; bone fractures; bone resorption; rickets; osteitis fibrosa cystica; fibrogenesis imperfect ossium; osteosclerosis; osteoporosis; osteomalacia; elevated parathyroid hormone levels; parathyroid gland hyperplasia; secondary hyperparathyroidism; hypocalcemia; infection; cancer; psoriasis; cardiovascular disease; renal osteodystrophy; renal disease; end-stage renal disease; chronic kidney disease; chronic kidney disease-associated mineral and bone disorder; extraskeletal calcification; obesity; allergy, asthama; multiple sclerosis; muscle weakness; rheumatoid arthritis and diabetes.

In some embodiments, the treatment can comprise administering a compound selected from the group consisting of: calcitriol; dihydrotachysterol; doxercalciferol; paricalcitol; cholecalciferol and ergocalciferol.

In another aspect, the invention relates to a method for treating a vitamin D insufficiency in a subject comprising detecting a level of VDBP polypeptide, albumin polypeptide and total vitamin D in a blood sample obtained from a subject; wherein a level of free vitamin D is: ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K _(DBP)}). and administering a treatment for vitamin D insufficiency to the subject if the level of free vitamin D is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of free vitamin D in a population of healthy subjects.

In some embodiments, the vitamin D can be selected from the group consisting of: 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.

In some embodiments, determining the level of VDBP polypeptide or albumin polypeptide can comprise the use of a method selected from the group consisting of: enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; immunoturbidimetric assay; immunonephelometric assay; dye-based photometric assay; western blot; immunoprecipitation; radioimmunological assay (RIA); radioimmunometric assay; immunofluorescence assay and mass spectroscopy.

In some embodiments, determining the level of total vitamin D can comprise the use of a method selected from the group consisting of: radioimmunoassay; liquid chromatography tandem mass spectroscopy; enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; and high-pressure liquid chromatography.

In some embodiments, an insufficiency of vitamin D can indicate an increased risk of a condition selected from the group consisting of: decreased bone density; decreased bone mineral density; bone fractures; bone resorption; rickets; osteitis fibrosa cystica; fibrogenesis imperfect ossium; osteosclerosis; osteoporosis; osteomalacia; elevated parathyroid hormone levels; parathyroid gland hyperplasia; secondary hyperparathyroidism; hypocalcemia; infection; cancer; psoriasis; cardiovascular disease; renal osteodystrophy; renal disease; end-stage renal disease; chronic kidney disease; chronic kidney disease-associated mineral and bone disorder; extraskeletal calcification; obesity; allergy, asthama; multiple sclerosis; muscle weakness; rheumatoid arthritis and diabetes.

In some embodiments, the treatment can comprise administering a compound selected from the group consisting of: calcitriol; dihydrotachysterol; doxercalciferol; paricalcitol; cholecalciferol and ergocalciferol.

In another aspect, the invention relates to a system for obtaining data from at least one blood sample obtained from at least one subject, the system comprising: a determination module configured to receive the at least one blood sample and perform at least one analysis on the at least one blood sample to determine a level of bioavailable or free vitamin D in the sample; a storage device configured to store data output from said determination module; and a display module for displaying a content based in part on the data output from said determination module, wherein the content comprises a signal indicative of the level of bioavailable or free vitamin D.

In some embodiments, the system further comprises a means of inputting a value for the level of one or more of VDBP polypeptide, albumin polypeptide, and total vitamin D determined to be in a test sample. In some embodiments, the content displayed on said display module further comprises a signal indicative of the subject having an increased likelihood of a vitamin D insufficiency if the level of bioavailable or free vitamin D is determined to be lower than the 25^(th) percentile value, or than 25% of the mean value, of bioavailable vitamin D in a population of healthy subjects. In some embodiments, the content displayed on said display module further comprises a signal indicative of the subject being recommended to receive a treatment for vitamin D insufficiency.

In some embodiments, a level of free and/or bioavailable vitamin D lower than the 25^(th) percentile, or than 25% of the mean value, of free and/or bioavailable vitamin D in a population of healthy subjects can indicate that the subject has a vitamin D insufficiency. In some embodiments, the vitamin D can be selected from the group consisting of: 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.

In some embodiments, determining the level of VDBP polypeptide or albumin polypeptide can comprise the use of a method selected from the group consisting of: enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; immunoturbidimetric assay; immunonephelometric assay; dye-based photometric assay; western blot; immunoprecipitation; radioimmunological assay (RIA); radioimmunometric assay; immunofluorescence assay and mass spectroscopy.

In some embodiments, determining the level of total vitamin D can comprise the use of a method selected from the group consisting of: radioimmunoassay; liquid chromatography tandem mass spectroscopy; enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; and high-pressure liquid chromatography.

In some embodiments, an insufficiency of vitamin D can indicate an increased risk of a condition selected from the group consisting of: decreased bone density; decreased bone mineral density; bone fractures; bone resorption; rickets; osteitis fibrosa cystica; fibrogenesis imperfect ossium; osteosclerosis; osteoporosis; osteomalacia; elevated parathyroid hormone levels; parathyroid gland hyperplasia; secondary hyperparathyroidism; hypocalcemia; infection; cancer; psoriasis; cardiovascular disease; renal osteodystrophy; renal disease; end-stage renal disease; chronic kidney disease; chronic kidney disease-associated mineral and bone disorder; extraskeletal calcification; obesity; allergy, asthama; multiple sclerosis; muscle weakness; rheumatoid arthritis and diabetes.

In some embodiments, the invention can further comprise the step of administering a vitamin D insufficiency treatment to a subject who is determined to have a vitamin D insufficiency. In some embodiments, the treatment can comprise administering a compound selected from the group consisting of: calcitriol; dihydrotachysterol; doxercalciferol; paricalcitol; cholecalciferol and ergocalciferol.

In another aspect, the invention relates to a method of treatment comprising: analyzing a blood sample obtained from a subject to determine a level of free or bioavailable vitamin D; wherein a level of free or bioavailable vitamin D lower than the 25^(th) percentile, or than 25% of the mean value of free or bioavailable vitamin D in a population of healthy subjects indicates that the subject has a vitamin D insufficiency; and administering a vitamin D insufficiency treatment to a subject who is determined to have a vitamin D insufficiency.

In some embodiments, the vitamin D can be selected from the group consisting of: 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.

In some embodiments, determining of the level of free and/or bioavailable vitamin D can comprise the use of a method selected from the group consisting of: immunoassay; two-step immnunoassay with antibody capture; one-step immunoassay with immobilized antibody and competitive detection; one-step immunoassay with immobilized competitor and labeled antibody; fluorescence polarization immunoassay; differential precipitation (immunoprecipitation, affinity precipitation); fluorescence polarization VDBP binding assay; immunodepletion; and affinity binding chromatography; and a method selected from the group consisting of: radioimmunoassay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; liquid chromatography tandem mass spectroscopy and high-pressure liquid chromatography.

In some embodiments of all of the methods described herein, determining a level of free and/or bioavailable vitamin D can comprise the use of chemically labeled 25-hydrovitamin D3 or vitamin D analogs with VDBP binding affinity. These chemical modifications to incorporate labeling moieties may first involve succinylation of the 3-hydroxyl group to yield 25-hydroxyvitamin D-3-hemisuccinate (Bouillon et al., Clin Chem. 1984 November; 30(11):1731-6). This succinylation modification provides a linker group ending with a carboxyl moiety that can be further derivatized with carboxyl-reactive compounds that are chromatophoric, fluorescent, luminescent, chemiluminescent, electroluminescent, or linked to enzymes. The labeling reaction of the carboxyl group on 25-hydroxyvitamin D-3-hemisuccinate can be modified directly, e.g., with labeling moieties containing diazoalkanes or alkyl halides; they can also be labeled by hydrazines, hydroxylamines, or primary amines in the presence of carbodiimide.

In some embodiments, an insufficiency of vitamin D can indicate an increased risk of a condition selected from the group consisting of: decreased bone density; decreased bone mineral density; bone fractures; bone resorption; rickets; osteitis fibrosa cystica; fibrogenesis imperfect ossium; osteosclerosis; osteoporosis; osteomalacia; elevated parathyroid hormone levels; parathyroid gland hyperplasia; secondary hyperparathyroidism; hypocalcemia; infection; cancer; psoriasis; cardiovascular disease; renal osteodystrophy; renal disease; end-stage renal disease; chronic kidney disease; chronic kidney disease-associated mineral and bone disorder; extraskeletal calcification; obesity; allergy, asthama; multiple sclerosis; muscle weakness; rheumatoid arthritis and diabetes.

In some embodiments, the treatment can comprise administering a compound selected from the group consisting of: calcitriol; dihydrotachysterol; doxercalciferol; paricalcitol; cholecalciferol and ergocalciferol.

In another aspect, the invention relates to an assay comprising analyzing a blood sample obtained from a subject to determine a level of free vitamin D and albumin polypeptide; wherein a level of bioavailable vitamin D is: =(K _(alb)*[Alb]+1)*[Free Vitamin D].

In some embodiments, a level of bioavailable vitamin D lower than the 25^(th) percentile, or than 25% of the mean value, of bioavailable vitamin D in a population of healthy subjects can indicate that the subject has a vitamin D insufficiency. In some embodiments, the vitamin D can be selected from the group consisting of: 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.

In some embodiments, determining the level of albumin polypeptide can comprise the use of a method selected from the group consisting of: enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; immunoturbidimetric assay; immunonephelometric assay; dye-based photometric assay; western blot; immunoprecipitation; radioimmunological assay (RIA); radioimmunometric assay; immunofluorescence assay and mass spectroscopy.

In some embodiments, determining of the level of free and/or bioavailable vitamin D can comprise the use of a method selected from the group consisting of: immunoassay; two-step immnunoassay with antibody capture; one-step immunoassay with immobilized antibody and competitive detection; one-step immunoassay with immobilized competitor and labeled antibody; fluorescence polarization immunoassay; differential precipitation (immunoprecipitation, affinity precipitation); immunodepletion; and affinity binding chromatography; and a method selected from the group consisting of: radioimmunoassay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; liquid chromatography tandem mass spectroscopy and high-pressure liquid chromatography.

Also provided herein are methods for treating a Vitamin D insufficiency in a subject. The methods include determining a level of bioavailable Vitamin D in the subject, by directly detecting levels of free Vitamin D and Vitamin D bound to albumin in a sample comprising serum or plasma from the subject using a differential affinity precipitation assay; comparing the level of bioavailable Vitamin D in the sample to a reference level of Vitamin D; identifying a subject who has a level of bioavailable Vitamin D below the reference level of Vitamin D as having a Vitamin D insufficiency; and administering a vitamin D insufficiency treatment to a subject identified as having a vitamin D insufficiency. In some embodiments, a Vitamin D Index is calculated in the subject and compared to a reference Index, below which a subject is identified as having a Vitamin D insufficiency, and a vitamin D insufficiency treatment is administered to a subject who has a Vitamin D Index below the reference Index.

In some embodiments, the differential affinity precipitation assay is performed by a method comprising contacting a sample comprising serum or plasma from the subject with purified Vitamin D Binding Polypeptide (VDBP), wherein the purified VDBP is immobilized on a substrate (e.g., beads, solid surface) for a time sufficient for free and albumin-bound Vitamin D in the sample to bind to the purified VDBP, thereby forming a test sample Vitamin D-VDBP complexes; optionally removing any Vitamin D not bound to the purified VDBP from the test sample; contacting the Vitamin D-VDBP complexes with a known amount of free labeled Vitamin D, for a time sufficient for the labeled Vitamin D to equilibrate with the Vitamin D-VDBP complexes in the test sample; determining the amount of labeled Vitamin D bound to the purified VDBP in the test sample, and calculating the amount of bioavailable Vitamin D in the sample from the subject based on the amount of labeled Vitamin D bound to the purified VDBP in the test sample.

The VDBP can be immobilized on a substrate using any method known in the art. In some embodiments, the VDBP can be immobilized on a substrate coated with gold, biotin streptavidin, N-hydroxysuccinimide or oxirane or other amine-reactive linker molecules, hydrazine or hydroxylamine or other carboxyl-reactive linker molecules, maleimide or other thiol-reactive linker molecules, or another molecule suitable for immobilizing the VDBP. In some embodiments, the VDBP is a fusion protein and comprises a peptide immobilization moiety, e.g., Argtag, calmodulin-binding peptide, cellulose-binding domain, DsbA, c-myc-tag, glutathione S-transferase, FLAG-tag, HAT-tag, polyhistidine-tag, maltose-binding protein, NusA, Stag, SBP-tag, Strep-tag, MBP, SUMO, Protein A, Protein G, and/or thioredoxin, and the substrate is coated with the partner for the immobilization moiety; see, e.g., Terpe, Appl Microbiol Biotechnol (2003) 60:523-533. In some embodiments, the VDBP are immobilized on the substrate via direct adsorption, peptide linkers, disulfide, maleimide, vinyl sulfone, or haloacetyl chemistries. For example, N- or C-terminal cysteine residues can be added to the VDBP using standard techniques of molecular biology, allowing the modified VDBP to be attached directly to gold surfaces, or indirectly to suitably modified glass or plastic surfaces, e.g., surfaces modified by introduction of disulfide, maleimide, vinyl sulfone, and/or haloacetyl chemistries. An azido group can be added, e.g., using the method of expressed protein ligation and a synthetic bifunctional reagent. This azido protein can be immobilized by Staudinger ligation. In some embodiments, the VDBP is covalently bound to the surface.

The beads or solid substrate can be any known in the art, including microarrays (e.g., as described herein), polymeric beads (e.g., polystyrene, acrylamide, acrylamide-azlactone), agarose beads (e.g., activated agarose that allows direct binding of the VDBP to the bead, e.g., tosyl activated agarose), paramagnetic beads, multiwall plates, or other surfaces. In some embodiments the surface is a magnetic or paramagnetic bead. In some embodiments the surface is a porous gel support, e.g., sugar- or acrylamide-based polymer resins or beads.

In some embodiments, an insufficiency of vitamin D can indicate an increased risk of a condition selected from the group consisting of: decreased bone density; decreased bone mineral density; bone fractures; bone resorption; rickets; osteitis fibrosa cystica; fibrogenesis imperfect ossium; osteosclerosis; osteoporosis; osteomalacia; elevated parathyroid hormone levels; parathyroid gland hyperplasia; secondary hyperparathyroidism; hypocalcemia; infection; cancer; psoriasis; cardiovascular disease; renal osteodystrophy; renal disease; end-stage renal disease; chronic kidney disease; chronic kidney disease-associated mineral and bone disorder; extraskeletal calcification; obesity; allergy, asthama; multiple sclerosis; muscle weakness; rheumatoid arthritis and diabetes.

In some embodiments, the invention can further comprise the step of administering a vitamin D insufficiency treatment to a subject who is determined to have a vitamin D insufficiency. In some embodiments, the treatment can comprise administering a compound selected from the group consisting of: calcitriol; dihydrotachysterol; doxercalciferol; paricalcitol; cholecalciferol and ergocalciferol.

In some embodiments, the invention can further comprise the measurement of total serum or plasma 25-hydroxyvitamin D combined with analysis of patients' vitamin D binding protein variant genotypes as described herein in order to interpret total 25-hydroxyvitamin D levels using genotype-specific reference levels, e.g., thresholds or intervals. Analysis of patients' VDBP variant genotype may be achieved by analyzing for the presence of the Gc1F, Gc1S, or Gc2 protein variants using chromatography, mass spectrometry, antibodies directed against the specific variants, or by genotyping patients' DNA at their GC locus.

Thus, in another aspect, the invention includes methods for diagnosing and optionally treating a vitamin D insufficiency in a subject. The methods include determining a VDBP genotype in the subject, e.g., by determining the identity of both alleles of one or both of the SNPs listed in Table A in a sample from the subject; determining a level of total vitamin D, and/or a level of free and/or bioavailable vitamin D, in a sample from the subject; and comparing the level of total, free, and/or bioavailable vitamin D to a reference level for the subject's genotype; wherein the presence of a level of total, free, and/or bioavailable vitamin D below the reference level indicates that the subject has a vitamin D insufficiency. In some embodiments, the methods further include administering a treatment for vitamin D insufficiency as known in the art or described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts the relationship between total and free 25-hydroxyvitamin D and lumbar spine bone mineral density. DBP-Bound, Free, and Bioavailable 25-hydroxyvitamin D (25(OH)D) levels and the Vitamin D Index were calculated from measured total 25(OH)D and vitamin D binding protein (DBP) levels. Total 25(OH)D and DBP-bound 25(OH)D were not associated with lumbar spine bone mineral density (BMD). Free 25(OH)D, bioavailable 25(OH) D, and Vitamin D Index values were positively correlated with lumbar spine BMD.

FIG. 2 depicts the relationship between total or bioavailable 25(OH)D and serum calcium. Total levels of 25(OH)D demonstrated no association with serum calcium levels (corrected for albumin) while bioavailable 25(OH)D levels were positively associated with serum calcium.

FIG. 3 depicts the relationship between total or bioavailable 25(OH)D and PTH. After adjustment for age, gender, race, and survival status at one year, bioavailable 25(OH)D was significantly negatively associated with PTH levels, while total 25(OH)D demonstrated no association with PTH.

FIG. 4 depicts sample selection for Example 2. 25(OH)D and 1,25(OH)2D were previously measured as part of a case-control study within the ArMORR cohort. Equal numbers of cases (subjects who died within their first year on dialysis) and controls were randomly selected from each racial group.

FIG. 5 depicts hypotheses tested in Example 4.

FIG. 6 is a diagram of an embodiment of a system for performing an assay for determining the level of bioavailable or free vitamin D in a blood sample obtained from a subject.

FIG. 7 is a diagram of an embodiment of a comparison module as described herein.

FIG. 8 is a diagram of an embodiment of an operating system and applications for a computing system as described herein.

FIG. 9A is a schematic showing variant VDBP proteins among black and white homozygotes.

FIG. 9B is a bar graph showing bioavailable 25-hydroxyvitamin D levels in black and white homozygotes.

FIG. 9C is a schematic showing Vitamin D Binding Protein Variants result in similar bioavailable 25(OH)D levels in blacks and whites.

FIG. 10 is a graph showing the percent bioavailable 25(OH)D radioligand measurements in VDBP calibrators.

FIG. 11 is a graph showing Vitamin D radioligand competitive binding assay standard curve for conversion of radioligand binding measurements into equivalent calculated bioavailable 25(OH)D values.

FIG. 12 is a graph showing correlations between calculated bioavailable 25(OH)D concentrations in subjects homozygous for VDBP protein variants Gc1F, Gc1S, and Gc2, compared to measurements by radioligand competitive binding assay.

FIG. 13 is a schematic illustration of an exemplary differential affinity precipitation assay for bioavailable 25-hydroxyvitamin D.

FIG. 14 is a schematic illustration of an exemplary fluorescence polarization assay for bioavailable and VDBP-bound 25-hydroxyvitamin D.

FIG. 15 is a graph showing measurements of bioavailable 25-hydroxyvitamin D by affinity binding chromatography using immobilized purified DBP to extract bioavailable 25(OH)D from a standard solution and from human serum. The data shows that increasing amounts of soluble DBP in samples decreases the amounts of affinity-extracted bioavailable 25(OH)D.

DETAILED DESCRIPTION OF THE INVENTION

Aspects of the invention described herein include assays. Systems, and methods of treatment which are based on the inventors' discovery that total serum levels of vitamin D, the currently used clinical parameter, correlate poorly with measures of health such as bone mineral density and parathyroid hormone levels. The inventors have found that levels of bioavailable and free vitamin D correlate better with the same measures of health and are therefore more indicative of whether a subject has sufficient vitamin D levels. Described herein are assays for measuring bioavailable and free vitamin D and methods of treating subjects for vitamin D insufficiency.

Materials, procedures and considerations necessary to understand and use the disclosed methods are described in the following, as are experimental results and non-limiting examples that demonstrate and illustrate various embodiments of the methods and assays described.

Definitions

For convenience, certain terms employed herein, in the specification, examples and appended claims are collected here. Unless stated otherwise, or implicit from context, the following terms and phrases include the meanings provided below. Unless explicitly stated otherwise, or apparent from context, the terms and phrases below do not exclude the meaning that the term or phrase has acquired in the art to which it pertains. The definitions are provided to aid in describing particular embodiments, and are not intended to limit the claimed invention, because the scope of the invention is limited only by the claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

As used herein the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are essential to the method or composition, yet open to the inclusion of unspecified elements, whether essential or not.

As used herein the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment.

The term “consisting of” refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.

As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus for example, references to “the method” includes one or more methods, and/or steps of the type described herein and/or which will become apparent to those persons skilled in the art upon reading this disclosure and so forth. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The abbreviation, “e.g.” is derived from the Latin exempli gratia, and is used herein to indicate a non-limiting example. Thus, the abbreviation “e.g.” is synonymous with the term “for example.”

Definitions of common terms in cell biology and molecular biology can be found in “The Merck Manual of Diagnosis and Therapy”, 19th Edition, published by Merck Research Laboratories, 2006 (ISBN 0-911910-19-0); Robert S. Porter et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); The ELISA guidebook (Methods in molecular biology 149) by Crowther J. R. (2000); Fundamentals of RIA and Other Ligand Assays by Jeffrey Travis, 1979, Scientific Newsletters; Immunology by Werner Luttmann, published by Elsevier, 2006. Definitions of common terms in molecular biology can also be found in Benjamin Lewin, Genes X, published by Jones & Bartlett Publishing, 2009 (ISBN-10: 0763766321); Kendrew et al. (eds.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8) and Current Protocols in Protein Sciences 2009, Wiley Intersciences, Coligan et al., eds.

The terms “decrease,” “reduce,” “reduced”, “reduction”, “decrease,” and “inhibit” are all used herein generally to mean a decrease by a statistically significant amount relative to a reference. However, for avoidance of doubt, “reduce,” “reduction” or “decrease” or “inhibit” typically means a decrease by at least 10% as compared to a reference level and can include, for example, a decrease by at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, up to and including, for example, the complete absence of the given entity or parameter as compared to a reference level, or any decrease between 10-99% as compared to a reference level.

The terms “increased”, “increase” or “enhance” or “activate” or “promote” are all used herein to generally mean an increase by a statically significant amount: for the avoidance of any doubt, the terms “increased”, “increase” or “enhance” or “activate” or “promote” means an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level.

As used herein, the term “proteins” and “polypeptides” are used interchangeably herein to designate a series of amino acid residues connected to the other by peptide bonds between the alpha-amino and carboxy groups of adjacent residues. The terms “protein”, and “polypeptide”, which are used interchangeably herein, refer to a polymer of protein amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogs, regardless of its size or function. “Protein” and “polypeptide” are often used in reference to relatively large polypeptides, whereas the term “peptide” is often used in reference to small polypeptides, but usage of these terms in the art overlaps. The terms “protein” and “polypeptide” are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogs of the foregoing.

As used herein, an “allele” is one of a pair or series of genetic variants of a polymorphism at a specific genomic location.

As used herein, “genotype” refers to the diploid combination of alleles for a given genetic polymorphism. A homozygous subject carries two copies of the same allele and a heterozygous subject carries two different alleles.

As used herein, a “haplotype” is one or a set of signature genetic changes (polymorphisms) that are normally grouped closely together on the DNA strand, and are usually inherited as a group; the polymorphisms are also referred to herein as “markers.” A “haplotype” as used herein is information regarding the presence or absence of one or more genetic markers in a given chromosomal region in a subject. A haplotype can consist of a variety of genetic markers, including indels (insertions or deletions of the DNA at particular locations on the chromosome); single nucleotide polymorphisms (SNPs) in which a particular nucleotide is changed; microsatellites; and minisatellites.

The term “gene” refers to a DNA sequence in a chromosome that codes for a product (either RNA or its translation product, a polypeptide). A gene contains a coding region and includes regions preceding and following the coding region (termed respectively “leader” and “trailer”). The coding region is comprised of a plurality of coding segments (“exons”) and intervening sequences (“introns”) between individual coding segments.

The term “probe” refers to an oligonucleotide. A probe can be single stranded at the time of hybridization to a target. As used herein, probes include primers, i.e., oligonucleotides that can be used to prime a reaction, e.g., a PCR reaction.

The term “label” or “label containing moiety” refers in a moiety capable of detection, such as a radioactive isotope or group containing same, and nonisotopic labels, such as enzymes, biotin, avidin, streptavidin, digoxygenin, luminescent agents, dyes, haptens, and the like. Luminescent agents, depending upon the source of exciting energy, can be classified as radioluminescent, chemiluminescent, bioluminescent, and photoluminescent (including fluorescent and phosphorescent). A probe described herein can be bound, e.g., chemically bound to label-containing moieties or can be suitable to be so bound. The probe can be directly or indirectly labeled.

The term “direct label probe” (or “directly labeled probe”) refers to a nucleic acid probe whose label after hybrid formation with a target is detectable without further reactive processing of hybrid. The term “indirect label probe” (or “indirectly labeled probe”) refers to a nucleic acid probe whose label after hybrid formation with a target is further reacted in subsequent processing with one or more reagents to associate therewith one or more moieties that finally result in a detectable entity.

The terms “target,” “DNA target,” or “DNA target region” refers to a nucleotide sequence that occurs at a specific chromosomal location. Each such sequence or portion is preferably at least partially, single stranded (e.g., denatured) at the time of hybridization. When the target nucleotide sequences are located only in a single region or fraction of a given chromosome, the term “target region” is sometimes used. Targets for hybridization can be derived from specimens which include, but are not limited to, chromosomes or regions of chromosomes in normal, diseased or malignant human cells, either interphase or at any state of meiosis or mitosis, and either extracted or derived from living or postmortem tissues, organs or fluids; germinal cells including sperm and egg cells, or cells from zygotes, fetuses, or embryos, or chorionic or amniotic cells, or cells from any other germinating body; cells grown in vitro, from either long-term or short-term culture, and either normal, immortalized or transformed; inter- or intraspecific hybrids of different types of cells or differentiation states of these cells; individual chromosomes or portions of chromosomes, or translocated, deleted or other damaged chromosomes, isolated by any of a number of means known to those with skill in the art, including libraries of such chromosomes cloned and propagated in prokaryotic or other cloning vectors, or amplified in vitro by means well known to those with skill; or any forensic material, including but not limited to blood, or other samples.

The term “hybrid” refers to the product of a hybridization procedure between a probe and a target.

The term “hybridizing conditions” has general reference to the combinations of conditions that are employable in a given hybridization procedure to produce hybrids, such conditions typically involving controlled temperature, liquid phase, and contact between a probe (or probe composition) and a target. Conveniently and preferably, at least one denaturation step precedes a step wherein a probe or probe composition is contacted with a target. Guidance for performing hybridization reactions can be found in Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (2003), 6.3.1-6.3.6. Aqueous and nonaqueous methods are described in that reference and either can be used. Hybridization conditions referred to herein are a 50% formamide, 2×SSC wash for 10 minutes at 45° C. followed by a 2×SSC wash for 10 minutes at 37° C.

Calculations of “identity” between two sequences can be performed as follows. The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second nucleic acid sequence for optimal alignment and non-identical sequences can be disregarded for comparison purposes). The length of a sequence aligned for comparison purposes is at least 30% (e.g., at least 40%, 50%, 60%, 70%, 80%, 90% or 100%) of the length of the reference sequence. The nucleotides at corresponding nucleotide positions are then compared. When a position in the first sequence is occupied by the same nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.

The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In some embodiments, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package, using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

The term “nonspecific binding DNA” refers to DNA which is complementary to DNA segments of a probe, which DNA occurs in at least one other position in a genome, outside of a selected chromosomal target region within that genome. An example of nonspecific binding DNA comprises a class of DNA repeated segments whose members commonly occur in more than one chromosome or chromosome region. Such common repetitive segments tend to hybridize to a greater extent than other DNA segments that are present in probe composition.

As used herein, “determining the identity of an allele” includes obtaining information regarding the identity, presence or absence of one or more specific alleles in a subject. Determining the identity of an allele can, but need not, include obtaining a sample comprising DNA from a subject, and/or assessing the identity, presence or absence of one or more genetic markers in the sample. The individual or organization who determines the identity of the allele need not actually carry out the physical analysis of a sample from a subject; the methods can include using information obtained by analysis of the sample by a third party. Thus the methods can include steps that occur at more than one site. For example, a sample can be obtained from a subject at a first site, such as at a health care provider, or at the subject's home in the case of a self-testing kit. The sample can be analyzed at the same or a second site, e.g., at a laboratory or other testing facility.

In some embodiments, to determine the identity of an allele or presence/absence of an allele or genotype described herein, a biological sample that includes nucleated cells (such as blood, a cheek swab or mouthwash) is prepared and analyzed for the presence or absence of preselected markers. Such diagnoses may be performed by diagnostic laboratories, or, alternatively, diagnostic kits can be manufactured and sold to health care providers or to private individuals for self-diagnosis. Diagnostic or prognostic tests can be performed as described herein or using well known techniques, such as described in U.S. Pat. No. 5,800,998.

Results of these tests, and optionally interpretive information, can be returned to the subject, the health care provider or to a third party payor. The results can be used in a number of ways. The information can be, e.g., communicated to the tested subject, e.g., with a prognosis and optionally interpretive materials that help the subject understand the test results and prognosis. The information can be used, e.g., by a health care provider, to determine whether to administer a specific drug, or whether a subject should be assigned to a specific category. e.g., a category associated with a specific disease endophenotype, or with drug response or non-response. The information can be used, e.g., by a third party payor such as a healthcare payer (e.g., insurance company or HMO) or other agency, to determine whether or not to reimburse a health care provider for services to the subject, or whether to approve the provision of services to the subject. For example, the healthcare payer may decide to reimburse a health care provider for treatments for vitamin D deficiency if the subject has vitamin D deficiency. The presence or absence of the allele or genotype in a patient may be ascertained by using any of the methods described herein.

As used herein, the term “pharmaceutical composition” refers to the active agent in combination with a pharmaceutically acceptable carrier as commonly used in the pharmaceutical industry.

The phrase “pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

The phrase “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient or is toxic to the subject, use thereof in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.

As used herein, a “subject” means a human or animal. Usually the animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon. Patient or subject includes any subset of the foregoing, e.g., all of the above. In certain embodiments, the subject is a mammal, e.g., a primate, e.g., a human.

Preferably, the subject is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but is not limited to these examples. Mammals other than humans can be advantageously used as subjects that represent animal models of vitamin D insufficiency. In addition, the methods described herein can be used to treat domesticated animals and/or pets. A subject can be male or female. A subject can be one who has been previously diagnosed with or identified as suffering from or having vitamin D insufficiency or one or more diseases or conditions associated with a vitamin D insufficiency, and optionally, but need not have already undergone treatment for vitamin D insufficiency or the one or more diseases or conditions associated with a vitamin D insufficiency. A subject can also be one who has been diagnosed with or identified as suffering from vitamin D insufficiency or one or more diseases or conditions associated with a vitamin D insufficiency, but who shows improvements in known vitamin D insufficiency risk factors as a result of receiving one or more treatments for vitamin D insufficiency or one or more diseases or conditions associated with a vitamin D insufficiency. Alternatively, a subject can also be one who has not been previously diagnosed as having vitamin D insufficiency or one or more diseases or conditions associated with a vitamin D insufficiency. For example, a subject can be one who exhibits one or more risk factors for vitamin insufficiency or one or more diseases or conditions associated with a vitamin D insufficiency or a subject who does not exhibit vitamin D insufficiency risk factors.

Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages can mean±1%.

The term “statistically significant” or “significantly” refers to statistical significance and generally means a difference of at least two standard deviations (2SD).

Vitamin D Insufficiency

Aspects of the invention described herein include assays directed to determining whether a subject has a vitamin D insufficiency and methods of treating these conditions. As used herein, “vitamin D” refers to any of several forms of D vitamins including vitamin D1, D2, D3, D4 and isomers or derivatives thereof. Non-limiting examples of forms of vitamin D include vitamin D2 (ergocalciferol) which is produced by plants, vitamin D3 (cholecalciferol) which is produced by animals. Both vitamin D2 and D3 are hydroxylated in the liver to form, respectively, 25(OH)D2 (25-hydroxyvitamin D2) and 25(OH)D3 (25-hydroxyvitamin D3 or calcidiol), which can be referred to collectively as 25(OH)D. 25(OH)D is the primary transport form of vitamin D in the body and is the prohormone of the active vitamin D hormones. Further hydroxylation, primarily in the kidneys, converts 25(OH)D to 1,25(OH)₂D (including 1,25(OH)₂D3 (calcitriol) and 1,25(OH)₂D2). All of the foregoing forms of vitamin D are encompassed by the term “vitamin D” as used herein. In some embodiments, the level of vitamin D that is determined is the level of 25-(OH)D. In some embodiments, the level of vitamin D that is determined is the level of 25-(OH)D2. In some embodiments, the level of vitamin D that is determined is the level of 25-(OH)D3. In some embodiments, the level of vitamin D that is determined is the level of 1,25-(OH)₂D. In some embodiments, the level of vitamin D that is determined is the level of 1,25-(OH)₂D2. In some embodiments, the level of vitamin D that is determined is the level of 1,25-(OH)₂D3.

Vitamin D hormones influence bone mineralization and a number of aspects of blood chemistry, including blood calcium levels and blood phosphorus levels. Diseases and conditions which are caused by or associated with insufficient levels of vitamin D are referred to herein as “vitamin D-associated diseases.” Insufficient levels of vitamin D are associated with secondary hyperparathyroidism, parathyroid gland hyperplasia, elevated parathyroid hormone levels, hypocalcemia, chronic kidney disease (CKD), renal disease, end-stage renal disease, chronic kidney disease-associated mineral and bone disorder, psoriasis, low bone mineral density, bone resorption and metabolic bone diseases such as fibrogenesis imperfecta ossium, osteitis fibrosa cystica, osteomalacia, rickets, osteoporosis, osteosclerosis, non-traumatic fractures of the spine and hip, renal osteodystrophy, and extraskeletal calcification. Secondary hyperparathyroidism (SHPT) increases bone turnover, and if left untreated, can impair mineralization and decrease bone mass. Patients with SHPT have increased bone turnover and decreased bone mass that can eventually progress to osteomalacia. Osteomalacia is a severe defect in or absence of bone mineralization occurring when both vitamin D and dietary calcium levels are markedly reduced. Osteoporosis, defined as a deficiency of normal bone within bone tissue, can result either from a low calcium diet with replete vitamin D levels or with low vitamin D and adequate dietary calcium. Low serum 25(OH)D increases the risk of osteoporotic fractures, especially in older adults, and vitamin D and calcium supplementation at sufficient doses reduces the risk. A number of “non-classical” biologic effects have been reported for vitamin D beyond its “classical” effects on the parathyroid hormone system. Such effects have been reported in connection with cellular growth and differentiation, cellular proliferation, red blood cell formation, hair growth, muscular function, blood pressure, fibrosis, the immune system and the cardiovascular system, including the renin-angiotensin system. Vitamin D insufficiency has been implicated in the development or progression of, for example, infection, cardiovascular disease, allergy, asthama obesity, diabetes, muscle weakness, multiple sclerosis, rheumatoid arthritis and cancer.

Vitamin D insufficiency can be caused by insufficient exposure to sunlight, insufficient dietary intake of vitamin D, or conditions or clinical procedures, such as bariatric surgery, that result in reduced intestinal absorption of fat soluble vitamins such as vitamin D. Vitamin D levels are traditionally measured as the level of total serum 25(OH)D. Although total serum 25(OH)D is currently the most widely accepted assay for determining vitamin D status, it is subject to tremendous variation in results and interpretation, and may not be clinically relevant across all populations. Aspects of the invention described herein are directed to an assay for determining whether a subject is vitamin D insufficient by measuring the levels of bioavailable or free vitamin D, as opposed to total serum vitamin D.

As used herein, “vitamin D insufficiency” refers to suboptimal levels of vitamin D that can be associated with an increased risk of developing one or more of the conditions or diseases in which low vitamin D levels have been implicated, which are described above herein. Subjects with a vitamin D insufficiency may not have any symptoms, markers or signs of a vitamin D-associated disease or may have symptoms, markers or signs of one or more vitamin D-associated diseases. A subject who has a vitamin D insufficiency can be a subject who has a level of bioavailable or free vitamin D which is lower than a threshold level, e.g., the 25th percentile value or 25% or lower than the mean level, of that form of vitamin D measured in a healthy population of subjects. For example, a subject who has a level of bioavailable or free vitamin D which is 25%, or 20% or 15% or 10% or 5% or lower than the mean level of that form of vitamin D in a population of healthy subjects has an insufficient level of vitamin D.

A healthy subject can be one who does not display any markers, signs or symptoms of a vitamin D-associated disease or condition and who is not at risk of having a vitamin D insufficiency. By way of non-limiting example, a healthy subject will not exhibit signs or symptoms of rickets, which include, for example delayed growth, pain in the spine, pelvis or legs, muscle weakness, or skeletal deformities such as bowed legs, abnormal curvature of the spine, thickened wrists and ankles, and/or projection of the breastbone. Risk factors for vitamin D insufficiency are well-known in the art and can include, but are not limited to, not drinking vitamin D fortified milk (e.g. lactose intolerant subjects, subjects with milk allergies, some vegetarians, and breast-fed infants); dark skin; old age (e.g. the elderly have a reduced ability to synthesize vitamin D and can be more likely to stay indoors), chronic or acute or severe illness (conditions which make it likely the subject will stay indoors, in hospitals, in intensive care facilities, or institutional and assisted-care facilities, including subjects with Alzheimer's disease or who are mentally ill); covering all exposed skin (such as members of certain religions or cultures); regular use of sunscreen (e.g., the application of sunscreen with a Sun Protection Factor (SPF) value of 8 reduces production of vitamin D by 95%, and higher SPF values may further reduce vitamin D); having or having been diagnosed with a fat malabsorption syndrome (including but not limited to cystic fibrosis, cholestatic liver disease, other liver disease, gallbladder disease, pancreatic enzyme deficiency, Crohn's disease, inflammatory bowel disease, sprue or celiac disease, or surgical removal of part or all of the stomach and/or intestines); having had small bowel resections; taking medications that increase the catabolism of vitamin D, including phenytoin, fosphenytoin, phenobarbital, carbamazepine, and rifampin; taking medications that reduce absorption of vitamin D, including cholestyramine, colestipol, orlistat, mineral oil, and fat substitutes; taking medications that inhibit activation of vitamin D, including ketoconazole; taking medications that decrease calcium absorption, including corticosteroids; having or having been diagnosed as having gum disease, diabetes mellitus, insulin resistance syndrome, endothelial dysfunction (vitamin D deposited in body fat stores is less bioavailable) cardiovascular disease, artherosclerosis heart failure or osteoporosis; being obese; or being a postmenopausal woman.

Bioavailable Vitamin D

The assays and methods of treatments described herein are based on the inventors' discovery that the level of bioavailable and/or free vitamin D in the blood of a subject has a more significant correlation to measures of health such as bone mineral density and parathyroid hormone levels than does the level of total serum vitamin D.

In the blood stream, vitamin D can exist in one of three states; 1) bound by vitamin D binding protein, 2) bound by albumin protein or 3) unbound. As used herein, “vitamin D binding protein”, “VDBP” or “DBP” refers to a polypeptide of any of SEQ ID NO: 1, 2 or 3 (NCBI Gene ID No: 2638) and naturally occurring variants (e.g. alleles), homologs and functional derivatives thereof. VDBP binds vitamin D tightly, with a K_(D)=0.7×10⁹ M⁻¹ (for human VDBP). The fraction of vitamin D which is bound to VDBP is referred to herein as “D_(VDBP)”, “D_(DBP)”, “Vitamin D_(DBP)” or “Vitamin D_(VDBP).” As used herein. “albumin” refers to the polypeptide of any of SEQ ID NO: 4, 5 or 6 (NCBI Gene ID No: 213) and naturally occurring variants (e.g. alleles), homologs and functional derivatives thereof. Albumin binds vitamin D less tightly than VDBP, with a K_(D)=6×10⁵ M⁻¹ (for human albumin). The fraction of vitamin D which is bound to albumin is referred to herein as “D_(albumin)”, “D_(Alb)”, “vitamin D_(albumin)” or “vitamin D_(Alb).” Unbound vitamin D is also referred to herein as “free vitamin D” or “D.” As used herein, “bioavailable vitamin D” refers to, collectively, free vitamin D and vitamin D bound to albumin. Bioavailable vitamin D does not comprise the fraction of vitamin D which is bound to VDBP. Bioavailable vitamin D is interchangeably referred to herein as “V_(Bio)” and “Vitamin D_(Bio)”.

An Assay for Bioavailable Vitamin D

Aspects of the invention described herein are directed to assays to determine the level of bioavailable and/or free vitamin D in a blood sample obtained from a subject.

In some embodiments, the level of bioavailable and/or free vitamin D is determined by first determining the level of VDBP polypeptide, albumin polypeptide and total vitamin D in a blood sample obtained from a subject. The level of free and bioavailable vitamin D can then be calculated using these values and the binding constants of VDBP and albumin for vitamin D. For human proteins, the binding constants are, respectively, 0.7×10⁹ M⁻¹ and 6×10⁵ M⁻¹.

As used herein a “blood sample” refers to any amount of blood or a fraction thereof that has been obtained from a subject. In some embodiments, the blood sample can comprise whole blood or a fraction thereof, e.g. serum or plasma. In some embodiments, the blood sample is contacted with an anticoagulant or preservative prior to performing an assay as described herein. Non-limiting examples of anticoagulants and preservatives include CPD, CP2D (Citrate Phosphate Double Dextrose), CPDA-1, CDP/ADSOL®, CDP/Optisol®, AS-3 (Additive Solution 3, Haemonetics Corp Braintree Mass.) and SAG-M.

In some embodiments, a blood sample can be stored prior to being used in an assay as described herein. In some embodiments the blood sample can be stored for any given period of time, e.g. minutes, hours, days, weeks, up to months, prior to use in an assay as described herein. In one embodiment, the blood sample is frozen. In one embodiment, the blood sample is not frozen.

In some embodiments, the assays described herein are performed on a whole blood sample. In some embodiments, the assays described herein are performed on the plasma fraction of a blood sample. In some embodiments, the assays described herein are performed on the serum fraction of a blood sample.

The level of VDBP and/or albumin polypeptide present in the blood sample obtained from a subject can be determined by any method for determining the level of a specific polypeptide known in the art. In some embodiments, the assay is performed on an automated analyzer. Non-limiting examples of methods that can be used in the methods and assays described herein include enzyme linked immunosorbent assay; dye-based photometric assay; western blot; immunoprecipitation; radioimmunological assay (RIA); radioimmunometric assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; immunoturbidimetric assay; immunonephelometric assay; immunofluorescence assay and mass spectroscopy. Various methods of producing antibodies with a known antigen (e.g. a peptide comprised by the polypeptides of SEQ ID Nos. 1-6 are well-known to those ordinarily skilled in the art (see Antibodies: A Laboratory Manual (Harlow & Lane eds., 1988), which is hereby incorporated by reference in its entirety). In particular, suitable antibodies may be produced by chemical synthesis, by intracellular immunization (i.e., intrabody technology), or preferably, by recombinant expression techniques. Methods of producing antibodies may further include the hybridoma technology well-known in the art. Antibodies specific for albumin and VDBP are commercially available (e.g. Cat. # ab112888 and ab23484, respectively, Abcam; Cambridge, Mass.).

In some embodiments, albumin levels can be determined by dye-based photometric assays on an automated analyzer. Dye-based photometric assays are commercially available (e.g. the Albumin FS™ kits; DiaSys Diagnostic Systems Gmb; Holzheim, Germany or the Albumin reagent, Cat #OSR6102; Beckman Coulter; Brea, Calif.). Automated analyzers are commercially available (e.g. the AU2700 or AU5400 from Beckman Coulter; Brea, Calif.). Systems which are designed specifically for the determination of serum albumin levels are also available commercially (e.g. the Careside Analyzer™, Careside Inc., Culver City, Calif.). In some embodiments, the level of albumin levels can be determined using immunoassays, e.g. the Human Serum Albumin ELISA Kit (Cat #1190; Alpha Diagnostic International; San Antonio, Tex.).

In some embodiments, VDBP levels can be determined by ELISA. ELISA assays for VDBP are commercially available (e.g. Cat #DVDBP0; R&D Systems; Minneapolis, Minn.). In some embodiments, the assay is conducted after diluting serum samples 1 to 2,000 in Calibrator Diluent RD6-11 (R&D Systems Part Number 895489). ELISA is a technique for detecting and measuring the concentration of an antigen using a labeled (e.g. enzyme linked) form of the antibody. There are different forms of ELISA, which are well known to those skilled in the art. The standard techniques known in the art for ELISA are described in “Methods in Immunodiagnosis”, 2nd Edition, Rose and Bigazzi, eds. John Wiley & Sons, 1980; Campbell et al., “Methods and Immunology”, W. A. Benjamin. Inc., 1964; and Oellerich, M. 1984, J. Clin. Chem. Clin. Biochem., 22:895-904; which are incorporated by reference herein in their entirety.

The level of total vitamin D present in the blood sample obtained from a subject can be determined by any method known in the art. Non-limiting examples of methods that can be used in the methods and assays described herein include radioimmunoassay; liquid chromatography tandem mass spectroscopy; enzyme linked immunosorbent assay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; and high-pressure liquid chromatography. In some embodiments, the level of total vitamin D in a sample is determined by liquid chromatography tandem mass spectrometry (LC-MS). In some embodiments, the level of total vitamin D in a sample is determined by high performance liquid chromatography/mass spectrophotometry. In some embodiments, the level of total vitamin D in a sample is determined by radioimmunoassay. In some embodiments, the level of total vitamin D in a sample is determined using a commercially available radioimmunoassay (e.g. DiaSorin Inc, Stillwater, Minn., USA). In some embodiments, the level of total vitamin D in a sample is determined using a commercially available immunluminometric assay (e.g. Cat No 310600; DiaSorin Inc.; Stillwater MIN). The method of measuring total vitamin D in a blood sample obtained from a subject can also include liquid chromatography tandem mass spectroscopy as described in U.S. Pat. No. 7,700,365, which is included by reference herein in its entirety.

Mass spectroscopy methods are well known in the art and have been used to quantify and/or identify biomolecules. In some embodiments, the signal strength of peak values from spectra of a first sample and a second sample can be compared (e.g., visually, by computer analysis etc.), to determine the relative amounts of particular biomolecules. Software programs such as the Biomarker Wizard program (Ciphergen Biosystems, Inc., Fremont. Calif.) can be used to aid in analyzing mass spectra.

In some embodiments, the level of total vitamin D which is determined can comprise one or more forms of vitamin D selected from the group consisting of 25-hydroxyvitamin D (25(OH)D); 1,25-dihydroxyvitamin D (1,25-(OH)₂D); 25(OH)D2; 25(OH)D3; 1,25(OH)₂D2; 1,25-(OH)D3; vitamin D1; vitamin D2; vitamin D3; vitamin D4; ergocalciferol; cholecalciferol; calcidiol and calcitriol. In some embodiments, the level of total vitamin D which is determined can comprise 25-hydroxyvitamin D (25(OH)D). In some embodiments, the level of total vitamin D which is determined can comprise 25-hydroxyvitamin D2 (25(OH)D2). In some embodiments, the level of total vitamin D which is determined can comprise 25-hydroxyvitamin D3 (25(OH)D3). In some embodiments, the level of total vitamin D which is determined can comprise 1,25-dihydroxyvitamin D (1,25-(OH)₂D). In some embodiments, the level of total vitamin D which is determined can comprise 1,25-dihydroxyvitamin D2 (1,25-(OH)₂D2). In some embodiments, the level of total vitamin D which is determined can comprise 1,25-dihydroxyvitamin D3 (1,25-(OH)₂D3).

In some embodiments, once the levels of VDBP polypeptide, albumin polypeptide and total vitamin D in a blood sample obtained from a subject are determined, the level of free and/or bioavailable vitamin D can be determined. The level of free vitamin D can be calculated using Equation 8, the derivation of which is described in Example 1 herein. Free Vitamin D={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K _(DBP)})  (Eq. 8)

The level of bioavailable vitamin D can be calculated using Equation 9, the derivation of which is described in Example 1 herein. Bioavailable Vitamin D=(K _(alb)·[Alb]+1)·[Free Vitamin D]  (Eq. 9)

In some embodiments, the level of free (unbound) and/or bioavailable vitamin D can be determined directly. In some embodiments, the level of free vitamin D can be determined directly and used to calculate the level of bioavailable vitamin D. In some embodiments, the level of free vitamin D and the level of albumin polypeptide can be determined directly and used to calculate the level of bioavailable vitamin D. As used herein “determined directly” refers to determining the level of a first form of a vitamin or polypeptide by measuring or detecting the level of the first form of a vitamin or polypeptide as opposed to calculating the level of the first form of a vitamin or polypeptide using the level of a second or further form of a vitamin or polypeptide which was directly determined.

Direct measurement of the level of free and/or bioavailable vitamin D can be accomplished by a number of methods. Non-limiting examples of methods for direct measurement of the level of free vitamin D include the following. 1) Vitamin D complexed with VDBP can be depleted from a sample using immunodepletion or affinity binding chromatography to deplete VDBP from the sample. The remaining vitamin D (the bioavailable fraction) can then be measured according to any of the methods described elsewhere herein. 2) Vitamin D complexed with VDBP can be depleted from a sample using differential precipitation of VDBP with antibodies (immunoprecipitation), actin (affinity precipitation) with or without precipitating buffers (e.g. polyethylene glycol, ammonium sulfate) followed by centrifugal separation from free and/or bioavailable vitamin D and measurement of remaining vitamin D fraction according to any of the methods described elsewhere herein. 3) Immunoassays can also be used (see for example, Ekins et al. J Endocrinol Invest. 9 Suppl 4:3-15. 1986; which is incorporated by reference herein in its entirety). Immunoassays capitalize on the idea that free analyte may be measured using lower affinity antibodies which do not “strip” the vitamin from its high affinity binding protein. Free and/or bioavailable vitamin D can be measured directly using several competitive immunoassay approaches described below and in (Christofides, Nic D. The Immunoassay Handbook, 3^(rd) Ed. Editor David Wild, Elsevier Ltd, 2005; which is incorporated by reference herein in its entirety) These methods are all based upon two principals: (1) Antibodies will differentiate between free and protein-bound analytes if the reaction conditions (pH, temperature, buffers) do not interfere with binding between the vitamin and its binding protein, and (2) The total antibody binding capacity (affinity constant times antibody concentration) does not significantly deplete the total vitamin D concentration and thus does not “strip” the protein-bound vitamin D. This may be achieved using an antibody with relatively low affinity (˜10¹⁰ L/M) for the vitamin D ligand and/or limited assay reaction times which allow for binding of free and albumin-bound vitamin D but are too short to allow dissociation of VDBP-bound vitamin D.

Specific immunoassay designs that can be used include the following: A) Two-step measurement of free and/or bioavailable vitamin D with antibody capture—(1) capture of free and/or bioavailable vitamin D with immobilized vitamin D-binding antibody, (2) wash away unbound vitamin D and VDBP, (3) detection of bound vitamin D by competitive binding with labeled vitamin D (or labeled vitamin D analog that also binds the antibody). B) One-step measurement of free and/or bioavailable vitamin D with immobilized vitamin D-binding antibody and competitive detection using labeled vitamin D (or labeled vitamin D analog). C) One-step measurement of free and/or bioavailable vitamin D with immobilized vitamin D or vitamin D analog and labeled vitamin D-binding antibody. Free and/or bioavailable vitamin D from a sample competes with the immobilized vitamin D for binding to the labeled antibody. D) One-step measurement of free and/or bioavailable vitamin D with fluorescence polarization immunoassay (Mendel C M. Clin Chem. 38(9):1916-7. 1992; which is incorporated by reference herein in its entirety). Free and/or bioavailable vitamin D and fluorescently labeled vitamin D analog compete for binding to antibody and polarized fluorescence indicates relative amount of free and/or bioavailable vitamin D competing for binding sites.

In some embodiments, determining of the level of free and/or bioavailable vitamin D can comprise the use of a method selected from the group consisting of: immunoassay; two-step immunoassay with antibody capture; one-step immunoassay with immobilized antibody and competitive detection; one-step immunoassay with immobilized competitior and labeled antibody; fluorescence polarization immunoassay; differential precipitation (immunoprecipitation, affinity precipitation); immunodepletion; and affinity binding chromatography; and a method selected from the group consisting of: radioimmunoassay; chemiluminescent immunosorbent assay; electrochemiluminescent immunosorbent assay; fluorescent immunosorbent assay; dye linked immunosorbent assay; liquid chromatography tandem mass spectroscopy and high-pressure liquid chromatography.

In some embodiments, determining the level of free and/or bioavailable vitamin D is performed directly using a differential precipitation assay. As noted above, VDBP binds vitamin D tightly, with a K_(D)=0.7×10⁹ M⁻¹ (for human VDBP). Albumin binds vitamin D less tightly than VDBP, with a K_(D)=6×10⁵ M⁻¹ (for human albumin). This difference in affinity is exploited in an assay in which the high-affinity VDBP is used to pull free and albumin-bound D out of a subject sample, and labeled D is used to compete and quantify the amount of free and albumin-bound D in the sample.

An exemplary differential precipitation assay is shown in FIG. 13. In some embodiments, purified VDBP is immobilized by coating it onto a surface, e.g., a bead or well of a microtiter plate. The subject sample is applied, preferably after dilution into a suitable buffer, e.g., PBS. After a time sufficient to allow the D in the sample to equilibrate onto the immobilized VDBP, the liquid in the sample can optionally be removed. A labeled, purified D is then applied (whether or not the liquid sample was removed), and again allowed to equilibrate. After equilibration, unbound labeled D is removed by washing the immobilized VDBP with appropriate buffer. The amount of affinity precipitated labeled D is then determined using a method appropriate for the label; in a preferred embodiment, the labeled D is radiolabeled and the amount of radiolabled D is determined using scintillation counting. In other embodiments, the D is fluorescently labeled (see, e.g., Shimizu et al., Anal Biochem. 1991 April; 194(1):77-81); alternatively the D can be labeled with a radiologically detectable tag; fluorescent tag; luminescent tag; or a colorimetric tag. The amount of immobilized labeled D is then used to determine the amount of free and albumin-bound vitamin D present in the subject sample; the fraction of labeled vitamin D competitor reagent that is immobilized indicates the level of vitamin D in the blood sample which is bioavailable

The labeled D can be, e.g., 25-hydroxyvitamin D, 1,25-dihydroxyvitamin D, or 24,25-dihydroxivitamin D. In some embodiments the vitamin D is chemically labeled 25-hydrovitamin D3 or vitamin D analogs with VDBP binding affinity. These chemical modifications to incorporate labeling moieties can include succinylation of the 3-hydroxyl group to yield 25-hydroxyvitamin D-3-hemisuccinate (Bouillon et al., Clin Chem. 1984 November; 30(11):1731-6). This succinylation modification provides a linker group ending with a carboxyl moiety which may be further derivatized with carboxyl-reactive compounds that are chromatophoric, fluorescent, luminescent, chemiluminescent, or linked to enzymes. The labeling reaction of the carboxyl group on 25-hydroxyvitamin D-3-hemisuccinate can be modified directly, e.g., with labeling moieties containing diazoalkanes or alkyl halides: they can also be labeled by hydrazines, hydroxylamines, or primary amines in the presence of carbodiimide.

In some embodiments, purified vitamin D, e.g., 25-hydroxyvitamin D, 1,25-dihydroxyvitamin D, or 24,25-dihydroxivitamin D, is immobilized, rather than the VDBP, and the VDBP is labeled.

In some embodiments, the methods include simply using a one-step homogeneous binding assay with fluorescence polarization detection of bound ligand. A schematic of an exemplary assay for vitamin D using fluorescence polarization is provided in FIG. 14. Fluorescence polarization is based on the principal wherein fluorophores are excited by polarized light of the appropriate wavelength, and if the rotational diffusion (via Brownian motion) of the fluorophore is slower than the half-life of its fluorescent emission, the light emitted retains the same angle of polarization as the excitation photon. In these embodiments, 25-hydroxyvitamin D is attached to a fluorescent label and added to patient serum or plasma diluted in appropriate buffer. The labeled ligand binds tightly to VDBP in the patient sample, slowing its rate of rotational diffusion. The free and albumin-associated labeled D, in contrast, is less restricted and thus has faster rates of rotational diffusion. The fluorescent labels on free and bound ligands are excited with polarized light of the appropriate wavelength, resulting in fluorescent emission at a second wavelength. When the labeled D is bound to VDBP, its decreased rate of rotational diffusion causes the emitted fluorescence to retain the same angle of polarity as the excitation photons. The emitted light is then filtered with an appropriately polarization filter, and the polarized fluorescent emission are measured with a photometer. In this way, the amounts of polarized fluorescent emissions are proportional to the amounts of labeled D that have bound to VDBP in patients' samples. The amount of unpolarized fluorescence, in contrast, is proportional to the concentrations of non-VDBP bound 25-hydroxyvitamin D. The ratio of unpolarized and polarized fluorescence is thusly proportional to the ratio of bioavailable versus VDBP-bound 25-hydroxyvitamin D. This methodology has been used to measure concentrations of serum free thyroid hormone (Mendel, Clin Chem. 1992 September; 38(9):1916-7); binding of fluorescently labeled estradiol to estrogen receptor (Parker et al., J Biomol Screen. 2000 April; 5(2):77-88); and serum free drug concentrations (Mathias and Jung, Anal Bioanal Chem. 2007 July; 388(5-6):1147-56). In some embodiments, the rotational diffusion of VDBP-bound labeled D may be further reduced by adding anti-VDBP antibodies to this homogeneous assay in order to further reduce the rotational diffusion rate of VDBP.

In some embodiments, the methods include determining the total amount of vitamin D present in the sample, e.g., using a method described herein.

In some embodiments, when the level of bioavailable or free vitamin D determined to be in the blood sample of a subject is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects, the subject is likely to have a vitamin D insufficiency. In some embodiments, when the level of bioavailable or free vitamin D determined to be in the blood sample of a subject is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects, the subject is indicated to have a vitamin D insufficiency. In some embodiments, when the level of bioavailable or free vitamin D determined to be in the blood sample of a subject is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects, the subject has an increased likelihood of having or developing a vitamin D-associated disease. In some embodiments, when the level of bioavailable or free vitamin D determined to be in the blood sample of a subject is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects, the subject is in need of a treatment for vitamin D insufficiency. In some embodiments, when the level of bioavailable or free vitamin D determined to be in the blood sample of a subject is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects, the subject has a greater likelihood of being in need of a treatment for vitamin D insufficiency.

In some embodiments, when the level of bioavailable or free vitamin D determined to be in the blood sample of a subject is above a threshold level, e.g., the 25th percentile value, or than 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects, the subject is not treated for vitamin D insufficiency.

Methods of Determining a VDBP Genotype in a Subject

In some aspects, the methods described herein include determining a VDBP genotype in a subject. As described herein, the VDBP genotype affects normal circulating concentrations of plasma VDBP as well as the binding affinity of the VDBP for vitamin D, and therefor affects the clinical relevance of determination of vitamin D levels.

The methods described herein include determining the VDBP genotype of a subject. In some embodiments, a VDBP genotype is determined by detecting the identity of both alleles of two common single nucleotide polymorphisms in the VDBP gene (rs4588 and rs7041) in an subject. Thus the methods can include obtaining and analyzing a sample from a subject. The SNPs, plus flanking sequences, are shown in the following table A:

TABLE A SEQ ID SNP SEQUENCE NO: rs4588 AGCAAAATTGCCTGATGCCACACCCA[A/C] 7 GGAACTGGCAAAGCTGGTTAACAAG rs7041 GAGCGACTAAAAGCAAAATTGCCTGA[G/T] 8 GCCACACCCACGGAACTGGCAAAGC

The following genotypes have been identified:

Gc1S variant of the Vitamin D binding protein, encoded by the GC gene containing the rs7041 single nucleotide polymorphisms, with a T>G substitution resulting in the substitution of Aspartic acid with glutamic acid at residue 416 of the VDBP polypeptide. The rs4588 single nucleotide polymorphism for Gc1S (C) is the ancestral allele encoding threonine at position 420.

Gc1F variant of the Vitamin D binding protein, encoded by the GC gene containing the ancestral alleles for both rs7041 and rs4588 single nucleotide polymorphisms; these alleles encode for aspartic acid and threonine at positions 416 and 420 of the VDBP polypeptide.

Gc2 variant of the Vitamin D binding protein, encoded by the GC gene containing the rs4588 SNP, with a C>A substitution resulting in the substitution of threonine acid with lysine at residue 420 of the VDBP polypeptide. The rs7041 single nucleotide polymorphism for Gc2 is the ancestral allele (T) encoding aspartic acid at position 416.

Gc1S variant of the Vitamin D binding protein, encoded by the GC gene containing the rs7041 SNP, with a T>G substitution resulting in the substitution of Aspartic acid with glutamic acid at residue 416 of the VDBP polypeptide.

Once the VDBP genotype for an individual subject is known, for patients who are homozygous for Gc1S/Gc1S, Gc1F/Gc1F, or Gc2/Gc2, the genotype-adjusted free and bioavailable fractions of 25-hydroxyvitamin D can be calculated using the known binding affinities for the three variants (Lauridsen et al., Clin Chem 2001; 47:753-6):

For subjects homozygous for Gc1F variant, KDBP=1.12×108M-1

For subjects homozygous for Gc1S variant, KDBP=0.60×108M-1

For subjects homozygous for Gc2 variant, KDBP=0.36×108M-1

Samples that are suitable for use in the methods described herein contain genetic material, e.g., genomic DNA (gDNA). Genomic DNA is typically extracted from biological samples such as blood or mucosal scrapings of the lining of the mouth, but can be extracted from other biological samples including urine or expectorant. The sample itself will typically consist of nucleated cells (e.g., blood or buccal cells) or tissue removed from the subject. The subject can be an adult, child, fetus, or embryo. In some embodiments, the sample is obtained prenatally, either from a fetus or embryo or from the mother (e.g., from fetal or embryonic cells in the maternal circulation). Methods and reagents are known in the art for obtaining, processing, and analyzing samples. In some embodiments, the sample is obtained with the assistance of a health care provider, e.g., to draw blood. In some embodiments, the sample is obtained without the assistance of a health care provider, e.g., where the sample is obtained non-invasively, such as a sample comprising buccal cells that is obtained using a buccal swab or brush, or a mouthwash sample. In some embodiments, the same sample that is used for the determination of free and/or bioavailable vitamin D is also used to detect the VDBP genotype in the subject.

In some cases, a biological sample may be processed for DNA isolation. For example, DNA in a cell or tissue sample can be separated from other components of the sample. Cells can be harvested from a biological sample using standard techniques known in the art. For example, cells can be harvested by centrifuging a cell sample and resuspending the pelleted cells. The cells can be resuspended in a buffered solution such as phosphate-buffered saline (PBS). After centrifuging the cell suspension to obtain a cell pellet, the cells can be lysed to extract DNA, e.g., gDNA. See, e.g., Ausubel et al., 2003, supra. The sample can be concentrated and/or purified to isolate DNA. All samples obtained from a subject, including those subjected to any sort of further processing, are considered to be obtained from the subject. Routine methods can be used to extract genomic DNA from a biological sample, including, for example, phenol extraction. Alternatively, genomic DNA can be extracted with kits such as the QIAamp® Tissue Kit (Qiagen, Chatsworth, Calif.) and the Wizard® Genomic DNA purification kit (Promega). Non-limiting examples of sources of samples include urine, blood, and tissue.

The absence or presence of an allele as described herein can be determined using methods known in the art. For example, gel electrophoresis, capillary electrophoresis, size exclusion chromatography, sequencing, and/or arrays can be used to detect the presence or absence of the allele or genotype. Amplification of nucleic acids, where desirable, can be accomplished using methods known in the art, e.g., PCR. In one example, a sample (e.g., a sample comprising genomic DNA), is obtained from a subject. The DNA in the sample is then examined to identify or detect the presence of an allele or genotype as described herein. The allele or genotype can be identified or determined by any method described herein, e.g., by sequencing or by hybridization of the gene in the genomic DNA, RNA, or cDNA to a nucleic acid probe, e.g., a DNA probe (which includes cDNA and oligonucleotide probes) or an RNA probe. The nucleic acid probe can be designed to specifically or preferentially hybridize with a particular polymorphic variant.

Other methods of nucleic acid analysis can include direct manual sequencing (Church and Gilbert, Proc. Natl. Acad. Sci. USA 81:1991-1995 (1988); Sanger et al., Proc. Natl. Acad. Sci. USA 74:5463-5467 (1977); Beavis et al., U.S. Pat. No. 5,288,644); automated fluorescent sequencing; single-stranded conformation polymorphism assays (SSCP) (Schafer et al., Nat. Biotechnol. 15:33-39 (1995)); clamped denaturing gel electrophoresis (CDGE); two-dimensional gel electrophoresis (2DGE or TDGE); conformational sensitive gel electrophoresis (CSGE); denaturing gradient gel electrophoresis (DGGE) (Sheffield et al., Proc. Natl. Acad. Sci. USA 86:232-236 (1989)); denaturing high performance liquid chromatography (DHPLC, Underhill et al., Genome Res. 7:996-1005 (1997)); infrared matrix-assisted laser desorption/ionization (IR-MALDI) mass spectrometry (WO 99/57318); mobility shift analysis (Orita et al., Proc. Natl. Acad. Sci. USA 86:2766-2770 (1989)); restriction enzyme analysis (Flavell et al., Cell 15:25 (1978); Geever et al., Proc. Natl. Acad. Sci. USA 78:5081 (1981)); quantitative real-time PCR (Raca et al., Genet Test 8(4):387-94 (2004)); heteroduplex analysis; chemical mismatch cleavage (CMC) (Cotton et al., Proc. Natl. Acad. Sci. USA 85:4397-4401 (1985)); RNase protection assays (Myers et al., Science 230:1242 (1985)); use of polypeptides that recognize nucleotide mismatches, e.g., E. coli mutS protein; allele-specific PCR, and combinations of such methods. See, e.g., Gerber et al., U.S. Patent Publication No. 2004/0014095 which is incorporated herein by reference in its entirety.

Sequence analysis can also be used to detect specific polymorphic variants. For example, polymorphic variants can be detected by sequencing exons, introns, 5′ untranslated sequences, or 3′ untranslated sequences. A sample comprising DNA or RNA is obtained from the subject. PCR or other appropriate methods can be used to amplify a portion encompassing the polymorphic site, if desired. The sequence is then ascertained, using any standard method, and the presence of a polymorphic variant is determined. Real-time pyrophosphate DNA sequencing is yet another approach to detection of polymorphisms and polymorphic variants (Alderborn et al., Genome Research 10(8):1249-1258 (2000)). Additional methods include, for example, PCR amplification in combination with denaturing high performance liquid chromatography (dHPLC) (Underhill et al., Genome Research 7(10):996-1005 (1997)).

In order to detect polymorphisms and/or polymorphic variants, it will frequently be desirable to amplify a portion of genomic DNA (gDNA) encompassing the polymorphic site. Such regions can be amplified and isolated by PCR using oligonucleotide primers designed based on genomic and/or cDNA sequences that flank the site. PCR refers to procedures in which target nucleic acid (e.g., genomic DNA) is amplified in a manner similar to that described in U.S. Pat. No. 4,683,195, and subsequent modifications of the procedure described therein. Generally, sequence information from the ends of the region of interest or beyond are used to design oligonucleotide primers that are identical or similar in sequence to opposite strands of a potential template to be amplified. See e.g., PCR Primer: A Laboratory Manual, Dieffenbach and Dveksler, (Eds.); McPherson et al., PCR Basics: From Background to Bench (Springer Verlag, 2000); Mattila et al., Nucleic Acids Res., 19:4967 (1991); Eckert et al., PCR Methods and Applications, 1:17 (1991); PCR (eds. McPherson et al., IRL Press, Oxford); and U.S. Pat. No. 4,683,202. Other amplification methods that may be employed include the ligase chain reaction (LCR) (Wu and Wallace, Genomics 4:560 (1989), Landegren et al., Science 241:1077 (1988), transcription amplification (Kwoh et al., Proc. Natl. Acad. Sci. USA 86:1173 (1989)), self-sustained sequence replication (Guatelli et al., Proc. Nat. Acad. Sci. USA 87:1874 (1990)), and nucleic acid based sequence amplification (NASBA). Guidelines for selecting primers for PCR amplification are well known in the art. See, e.g., McPherson et al., PCR Basics: From Background to Bench, Springer-Verlag, 2000. A variety of computer programs for designing primers are available, e.g., ‘Oligo’ (National Biosciences, Inc, Plymouth Minn.), MacVector (Kodak/IBI), and the GCG suite of sequence analysis programs (Genetics Computer Group, Madison, Wis. 53711).

In some cases, PCR conditions and primers can be developed that amplify a product only when the variant allele is present or only when the wild type allele is present (MSPCR or allele-specific PCR). For example, patient DNA and a control can be amplified separately using either a wild type primer or a primer specific for the variant allele. Each set of reactions is then examined for the presence of amplification products using standard methods to visualize the DNA. For example, the reactions can be electrophoresed through an agarose gel and the DNA visualized by staining with ethidium bromide or other DNA intercalating dye. In DNA samples from heterozygous patients, reaction products would be detected in each reaction.

Real-time quantitative PCR can also be used to determine copy number. Quantitative PCR permits both detection and quantification of specific DNA sequence in a sample as an absolute number of copies or as a relative amount when normalized to DNA input or other normalizing genes. A key feature of quantitative PCR is that the amplified DNA product is quantified in real-time as it accumulates in the reaction after each amplification cycle. Methods of quantification can include the use of fluorescent dyes that intercalate with double-stranded DNA, and modified DNA oligonucleotide probes that fluoresce when hybridized with a complementary DNA. Methods of quantification can include determining the intensity of fluorescence for fluorescently tagged molecular probes attached to a solid surface such as a microarray.

In some embodiments, a peptide nucleic acid (PNA) probe can be used instead of a nucleic acid probe in the hybridization methods described above. PNA is a DNA mimetic with a peptide-like, inorganic backbone, e.g., N-(2-aminoethyl)glycine units, with an organic base (A, G, C, T or U) attached to the glycine nitrogen via a methylene carbonyl linker (see, e.g., Nielsen et al., Bioconjugate Chemistry, The American Chemical Society, 5:1 (1994)). The PNA probe can be designed to specifically hybridize to a nucleic acid comprising a polymorphic variant conferring susceptibility to or indicative of the presence of a given VBDP genotype.

In some cases, allele-specific oligonucleotides can also be used to detect the presence of a polymorphic variant. For example, polymorphic variants can be detected by performing allele-specific hybridization or allele-specific restriction digests. Allele specific hybridization is an example of a method that can be used to detect sequence variants, including complete genotypes of a subject (e.g., a mammal such as a human). See Stoneking et al., Am. J. Hum. Genet. 48:370-382 (1991); and Prince et al., Genome Res. 11:152-162 (2001). An “allele-specific oligonucleotide” (also referred to herein as an “allele-specific oligonucleotide probe”) is an oligonucleotide that is specific for particular a polymorphism can be prepared using standard methods (see Ausubel et al., Current Protocols in Molecular Biology, supra). Allele-specific oligonucleotide probes typically can be approximately 10-50 base pairs, preferably approximately 15-30 base pairs, that specifically hybridizes to a nucleic acid region that contains a polymorphism. Hybridization conditions are selected such that a nucleic acid probe can specifically bind to the sequence of interest, e.g., the variant nucleic acid sequence. Such hybridizations typically are performed under high stringency as some sequence variants include only a single nucleotide difference. In some cases, dot-blot hybridization of amplified oligonucleotides with allele-specific oligonucleotide (ASO) probes can be performed. See, for example, Saiki et al., Nature (London) 324:163-166 (1986).

In some embodiments, allele-specific restriction digest analysis can be used to detect the existence of a polymorphic variant of a polymorphism, if alternate polymorphic variants of the polymorphism result in the creation or elimination of a restriction site. Allele-specific restriction digests can be performed in the following manner. A sample containing genomic DNA is obtained from the individual and genomic DNA is isolated for analysis. For nucleotide sequence variants that introduce a restriction site, restriction digest with the particular restriction enzyme can differentiate the alleles. In some cases, polymerase chain reaction (PCR) can be used to amplify a region comprising the polymorphic site, and restriction fragment length polymorphism analysis is conducted (see Ausubel et al., Current Protocols in Molecular Biology, supra). The digestion pattern of the relevant DNA fragment indicates the presence or absence of a particular polymorphic variant of the polymorphism and is therefore indicative of the presence of a specific VDBP genotype. For sequence variants that do not alter a common restriction site, mutagenic primers can be designed that introduce a restriction site when the variant allele is present or when the wild type allele is present. For example, a portion of a nucleic acid can be amplified using the mutagenic primer and a wild type primer, followed by digest with the appropriate restriction endonuclease.

In some embodiments, fluorescence polarization template-directed dye-terminator incorporation (FP-TDI) is used to determine which of multiple polymorphic variants of a polymorphism is present in a subject (Chen et al., Genome Research 9(5):492-498 (1999)). Rather than involving use of allele-specific probes or primers, this method employs primers that terminate adjacent to a polymorphic site, so that extension of the primer by a single nucleotide results in incorporation of a nucleotide complementary to the polymorphic variant at the polymorphic site.

In some cases. DNA containing an amplified portion may be dot-blotted, using standard methods (see Ausubel et al., Current Protocols in Molecular Biology, supra), and the blot contacted with the oligonucleotide probe. The presence of specific hybridization of the probe to the DNA is then detected. Specific hybridization of an allele-specific oligonucleotide probe (specific for a polymorphic variant shown in Table A) to DNA from the subject is indicative of the presence of a given VDBP genotype.

The methods typically include determining the genotype of a subject with respect to both copies of the polymorphic site present in the genome. For example, the complete genotype may be characterized as −/−, as −/+, or as +/+, where a minus sign indicates the presence of the reference or wild type sequence at the polymorphic site, and the plus sign indicates the presence of a polymorphic variant other than the reference sequence. If multiple polymorphic variants exist at a site, this can be appropriately indicated by specifying which ones are present in the subject. Any of the detection means described herein can be used to determine the genotype of a subject with respect to one or both copies of the polymorphism present in the subject's genome.

Additional methods of nucleic acid analysis to detect polymorphisms and/or polymorphic variants can include. e.g., microarray analysis. In some embodiments, it is desirable to employ methods that can detect the presence of multiple polymorphisms (e.g., polymorphic variants at a plurality of polymorphic sites) in parallel or substantially simultaneously. Oligonucleotide arrays represent one suitable means for doing so. Other methods, including methods in which reactions (e.g., amplification, hybridization) are performed in individual vessels, e.g., within individual wells of a multi-well plate or other vessel may also be performed so as to detect the presence of multiple polymorphic variants (e.g., polymorphic variants at a plurality of polymorphic sites) in parallel or substantially simultaneously according to certain embodiments.

Nucleic acid probes can be used to detect and/or quantify the presence of a particular target nucleic acid sequence within a sample of nucleic acid sequences, e.g., as hybridization probes, or to amplify a particular target sequence within a sample, e.g., as a primer. Probes have a complimentary nucleic acid sequence that selectively hybridizes to the target nucleic acid sequence. In order for a probe to hybridize to a target sequence, the hybridization probe must have sufficient identity with the target sequence, i.e., at least 70% (e.g., 80%, 90%, 95%, 98% or more) identity to the target sequence. The probe sequence must also be sufficiently long so that the probe exhibits selectivity for the target sequence over non-target sequences. For example, the probe will be at least 20 (e.g., 25, 30, 35, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900 or more) nucleotides in length. In some embodiments, the probes are not more than 30, 50, 100, 200, 300, 500, 750, or 1000 nucleotides in length. Probes are typically about 20 to about 1×106 nucleotides in length. Probes include primers, which generally refers to a single-stranded oligonucleotide probe that can act as a point of initiation of template-directed DNA synthesis using methods such as PCR (polymerase chain reaction), LCR (ligase chain reaction), etc., for amplification of a target sequence.

The probe can be a test probe such as a probe that can be used to detect polymorphisms in a region described herein (e.g., polymorphisms as described herein). For example, the probe can hybridize to an allele described herein, e.g., in Table A.

Control probes can also be used. For example, a probe that binds a less variable sequence, e.g., repetitive DNA associated with a centromere of a chromosome, can be used as a control. Probes that hybridize with various centromeric DNA and locus-specific DNA are available commercially, for example, from Vysis, Inc. (Downers Grove, Ill.), Molecular Probes, Inc. (Eugene, Oreg.), or from Cytocell (Oxfordshire, UK). Probe sets are available commercially such from Applied Biosystems, e.g., the Assays-on-Demand SNP kits Alternatively, probes can be synthesized, e.g., chemically or in vitro, or made from chromosomal or genomic DNA through standard techniques. For example, sources of DNA that can be used include genomic DNA, cloned DNA sequences, somatic cell hybrids that contain one, or a part of one, human chromosome along with the normal chromosome complement of the host, and chromosomes purified by flow cytometry or microdissection. The region of interest can be isolated through cloning, or by site-specific amplification via the polymerase chain reaction (PCR). See, for example, Nath and Johnson, Biotechnic. Histochem. 73(1):6-22 (1998); Wheeless et al., Cytometry 17:319-326 (1994); and U.S. Pat. No. 5,491,224.

In some embodiments, the probes are labeled, e.g., by direct labeling, with a fluorophore, an organic molecule that fluoresces after absorbing light of lower wavelength/higher energy. A directly labeled fluorophore allows the probe to be visualized without a secondary detection molecule. After covalently attaching a fluorophore to a nucleotide, the nucleotide can be directly incorporated into the probe with standard techniques such as nick translation, random priming, and PCR labeling. Alternatively, deoxycytidine nucleotides within the probe can be transaminated with a linker. The fluorophore then is covalently attached to the transaminated deoxycytidine nucleotides. See, e.g., U.S. Pat. No. 5,491,224.

Fluorophores of different colors can be chosen such that each probe in a set can be distinctly visualized. For example, a combination of the following fluorophores can be used: 7-amino-4-methylcoumarin-3-acetic acid (AMCA), TEXAS RED™ (Molecular Probes, Inc., Eugene, Oreg.), 5-(and-6)-carboxy-X-rhodanine, lissamine rhodamine B, 5-(and-6)-carboxyfluorescein, fluorescein-5-isothiocyanate (FITC), 7-diethylaminocoumarin-3-carboxylic acid, tetramethylrhodamine-5-(and-6)-isothiocyanate, 5-(and-6)-carboxytetramethylrhodamine, 7-hydroxycoumarin-3-carboxylic acid, 6-[fluorescein 5-(and-6)-carboxamido]hexanoic acid, N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a diaza-3-indacenepropionic acid, eosin-5-isothiocyanate, erythrosin-5-isothiocyanate, and CASCADE™ blue acetylazide (Molecular Probes, Inc., Eugene, Oreg.). Fluorescently labeled probes can be viewed with a fluorescence microscope and an appropriate filter for each fluorophore, or by using dual or triple band-pass filter sets to observe multiple fluorophores. See, for example, U.S. Pat. No. 5,776,688. Alternatively, techniques such as flow cytometry can be used to examine the hybridization pattern of the probes. Fluorescence-based arrays are also known in the art.

In other embodiments, the probes can be indirectly labeled with, e.g., biotin or digoxygenin, or labeled with radioactive isotopes such as 32P and 3H. For example, a probe indirectly labeled with biotin can be detected by avidin conjugated to a detectable marker. For example, avidin can be conjugated to an enzymatic marker such as alkaline phosphatase or horseradish peroxidase. Enzymatic markers can be detected in standard colorimetric reactions using a substrate and/or a catalyst for the enzyme. Catalysts for alkaline phosphatase include 5-bromo-4-chloro-3-indolylphosphate and nitro blue tetrazolium. Diaminobenzoate can be used as a catalyst for horseradish peroxidase.

In another aspect, this document features arrays that include a substrate having a plurality of addressable areas, and methods of using them. At least one area of the plurality includes a nucleic acid probe that binds specifically to a sequence comprising a polymorphism listed in Tables 1-2 or Table A, and can be used to detect the absence or presence of said polymorphism, e.g., one or more SNPs, microsatellites, minisatellites, or indels, as described herein, to determine or identify an allele or genotype. For example, the array can include one or more nucleic acid probes that can be used to detect a polymorphism listed in Table A. In some embodiments, the probes are nucleic acid capture probes.

Generally, microarray hybridization is performed by hybridizing a nucleic acid of interest (e.g., a nucleic acid encompassing a polymorphic site) with the array and detecting hybridization using nucleic acid probes. In some cases, the nucleic acid of interest is amplified prior to hybridization. Hybridization and detecting are generally carried out according to standard methods. See, e.g., Published PCT Application Nos. WO 92/10092 and WO 95/11995, and U.S. Pat. No. 5,424,186. For example, the array can be scanned to determine the position on the array to which the nucleic acid hybridizes. The hybridization data obtained from the scan is typically in the form of fluorescence intensities as a function of location on the array.

Arrays can be formed on substrates fabricated with materials such as paper, glass, plastic (e.g., polypropylene, nylon, or polystyrene), polyacrylamide, nitrocellulose, silicon, optical fiber, or any other suitable solid or semisolid support, and can be configured in a planar (e.g., glass plates, silicon chips) or three dimensional (e.g., pins, fibers, beads, particles, microtiter wells, capillaries) configuration. Methods for generating arrays are known in the art and include, e.g., photolithographic methods (see, e.g., U.S. Pat. Nos. 5,143,854; 5,510,270; and 5,527,681), mechanical methods (e.g., directed-flow methods as described in U.S. Pat. No. 5,384,261), pin-based methods (e.g., as described in U.S. Pat. No. 5,288,514), and bead-based techniques (e.g., as described in PCT US/93/04145). The array typically includes oligonucleotide hybridization probes capable of specifically hybridizing to different polymorphic variants. Oligonucleotide probes that exhibit differential or selective binding to polymorphic sites may readily be designed by one of ordinary skill in the art. For example, an oligonucleotide that is perfectly complementary to a sequence that encompasses a polymorphic site (i.e., a sequence that includes the polymorphic site, within it or at one end) will generally hybridize preferentially to a nucleic acid comprising that sequence, as opposed to a nucleic acid comprising an alternate polymorphic variant.

Oligonucleotide probes forming an array may be attached to a substrate by any number of techniques, including, without limitation, (i) in situ synthesis (e.g., high-density oligonucleotide arrays) using photolithographic techniques; (ii) spotting/printing at medium to low density on glass, nylon or nitrocellulose; (iii) by masking, and (iv) by dot-blotting on a nylon or nitrocellulose hybridization membrane. Oligonucleotides can be immobilized via a linker, including by covalent, ionic, or physical linkage. Linkers for immobilizing nucleic acids and polypeptides, including reversible or cleavable linkers, are known in the art. See, for example, U.S. Pat. No. 5,451,683 and WO98/20019. Alternatively, oligonucleotides can be non-covalently immobilized on a substrate by hybridization to anchors, by means of magnetic beads, or in a fluid phase such as in microtiter wells or capillaries. Immobilized oligonucleotide probes are typically about 20 nucleotides in length, but can vary from about 10 nucleotides to about 1000 nucleotides in length.

Arrays can include multiple detection blocks (i.e., multiple groups of probes designed for detection of particular polymorphisms). Such arrays can be used to analyze multiple different polymorphisms. Detection blocks may be grouped within a single array or in multiple, separate arrays so that varying conditions (e.g., conditions optimized for particular polymorphisms) may be used during the hybridization. For example, it may be desirable to provide for the detection of those polymorphisms that fall within G-C rich stretches of a genomic sequence, separately from those falling in A-T rich segments. General descriptions of using oligonucleotide arrays for detection of polymorphisms can be found, for example, in U.S. Pat. Nos. 5,858,659 and 5,837,832. In addition to oligonucleotide arrays, cDNA arrays may be used similarly in certain embodiments.

The methods described herein can include providing an array as described herein; contacting the array with a sample (e.g., a portion of genomic DNA that includes at least a portion of a human chromosome), and detecting binding of a nucleic acid from the sample to the array. Optionally, the method includes amplifying nucleic acid from the sample, e.g., genomic DNA that includes a portion of a human chromosome described herein prior to or during contact with the array.

In some aspects, the methods described herein can include using an array that can ascertain differential expression patterns or copy numbers of one or more genes in samples from normal and affected individuals (see, e.g., Redon et al., Nature 444(7118):444-54 (2006)). For example, arrays of probes to a marker described herein can be used to measure polymorphisms between DNA from a subject having a specific VBDP genotype, and control DNA, e.g., DNA obtained from an individual that does not that VBDP genotype. Since the clones on the array contain sequence tags, their positions on the array are accurately known relative to the genomic sequence. Methods for array production, hybridization, and analysis are described, e.g., in Snijders et al., Nat. Genetics 29:263-264 (2001); Klein et al., Proc. Natl Acad. Sci. USA 96:4494-4499 (1999); Albertson et al., Breast Cancer Research and Treatment 78:289-298 (2003); and Snijders et al., “BAC microarray based comparative genomic hybridization,” in: Zhao et al. (eds), Bacterial Artificial Chromosomes: Methods and Protocols, Methods in Molecular Biology, Humana Press, 2002.

In another aspect, this document provides methods of determining the absence or presence of a VBDP genotype as described herein, using an array described above. The methods can include providing a two dimensional array having a plurality of addresses, each address of the plurality being positionally distinguishable from each other address of the plurality having a unique nucleic acid capture probe, contacting the array with a sample from a test subject, and analyzing the binding of the sample to determine the VBDP genotype in the subject. In the case of a nucleic acid hybridization, binding with a capture probe at an address of the plurality, can be detected by any method known in the art, e.g., by detection of a signal generated from a label attached to the nucleic acid.

Alternatively or in addition, a subject's VDBP genotype can be determined by analysis of the protein product of the VDBP gene in the subject. Thus, for example, analysis of patients' VDBP variant genotype may be achieved by analyzing for the presence of the Gc1F, Gc1S, or Gc2 protein variants using chromatography, mass spectrometry, or antibodies directed against the specific variants.

A subject's VDBP genotype can be used in determining the reference value to which a level of total vitamin D, or of free and/or bioavailable vitamin D, is compared. Thus, in some embodiments, the methods include determining a test subject's VDBP; determining a level of total vitamin D, or of free and/or bioavailable vitamin D in a sample from the test subject; and comparing the level in the sample to a reference level for that genotype, e.g., a reference level determined for a subject who has the same genotype as the test subject. A reference level for a control subject who has the same genotype as the test subject can represent a threshold level below which a subject having that genotype is considered to have vitamin D insufficiency. Suitable reference levels that are genotype-specific can be determined using methods known in the art, e.g., including statistically determining an appropriate reference level in a cohort of subjects who have the same genotype as the test subject. For example, one reference level could be a level of total vitamin D, or of free and/or bioavailable vitamin D, lower than the 25^(th) percentile value or 25% of the mean value, of total vitamin D, or of free and/or bioavailable vitamin D, in a population of healthy subjects who have an identified genotype.

Other suitable reference levels that can be used in a method described herein include cutoff points for the lowest statistically determined interval or portion of the population, e.g., the bottom tertile, quartile, or quintile.

Methods of Treating Vitamin D Insufficiency

Aspects of the invention described herein are directed to methods of treating a vitamin D insufficiency comprising detecting the level of bioavailable or free vitamin D in a blood sample obtained from a subject and administering a treatment for vitamin D insufficiency if the level of bioavailable vitamin D is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable vitamin D in a population of healthy subjects. In some embodiments, the level of bioavailable or free vitamin D is determined by determining the level of VDBP polypeptide, albumin polypeptide and total vitamin D in a blood sample obtained from a subject and calculating the level of free and/or bioavailable vitamin D as described above herein. In some embodiments, the level of free (unbound) and/or bioavailable vitamin D can be determined directly. In some embodiments, the level of free vitamin D can be determined directly and used to calculate the level of bioavailable vitamin D. In some embodiments, the level of free vitamin D and the level of albumin polypeptide can be determined directly and used to calculate the level of bioavailable vitamin D.

In some embodiments, a treatment for vitamin D insufficiency can include, for example, compounds which increase the level of vitamin D, bioavailable vitamin D and/or free vitamin D in the subject by providing one or more forms of vitamin D, stimulating the endogenous production of vitamin D, stimulating the production of active forms of vitamin D and/or inhibiting the metabolism of vitamin D. Many naturally-occurring forms of vitamin D, derivatives and analogs thereof can be administered to subjects in need of a vitamin D insufficiency treatment. In some embodiments, any form of vitamin D or a derivative or analog thereof may be used provided that it exhibits one or more activities of naturally-occurring active vitamin D (e.g. increases intestinal calcium absorption, serum calcium levies or bone mineralization) or is metabolized to a compound that exhibits such activity. Non-limiting examples of such compounds include alfacalcidol; calcifediol; calcipotriene; calcidiol; calcitriol (Rocaltrol; Roche); dihydrotachysterol (DH™ and DHT Intensol™; Roxane Laboratories); doxercalciferol (Hectorol®; Genzyme); paricalcitol (Zemplar®; Abbott Laboratories); cholecalciferol (Delta D3™; Freeda Vitamins Inc.) and ergocalciferol 3?(Drisdol; Sanofi). Cholecalciferol and ergocalciferol are available as dietary supplements. Further non-limiting examples include 5,6-trans-cholecalciferols; 5,6-trans-ergocalciferols; fluorinated cholecalciferols; side chain homologated cholecalciferols; side chain-truncated cholecalciferols; 19-nor cholecalciferols and ergocalciferols; 10,19-dihydrovitamin D compounds; 25-hydroxyvitamin D3; 25-hydroxyvitamin D2; 24,24-difluoro-25-hydroxyvitamin D3; 24-fluoro-25-hydroxyvitamin D3; 26,26,26,27,27hexafluoro-25-hydroxyvitaminn D3; 24-25-dihydroxyvitamin D3; d5,26dihydroxyvitamin D3; 23,25,26-trihydroxyvitamin D3; 25-hydroxyvitamin D3; the side chain, nor, dinor, trinor and tetranoranalogs of 25-hydroxyvitamin D3, 24-homo-1,25-dihydroxyvitamin D3; 24-dihomo-1,25-dihydroxyvitamin D3; 24-trihomo-1,25-dihydroxyvitamin D3; as well as the corresponding 19-nor compounds of those listed above.

Vitamin D activity can be assayed by a number of methods known in the art. A non-limiting example of an assay to determine if a compound has vitamin D activity or is metabolized m the subject's body to a compound having vitamin D activity is described in U.S. Pat. No. 5,532,229 which is incorporated by reference herein in its entirety. Briefly, the compound is administered and the levels of serum calcium are determined by chemical colorimetry or by treating with nitric acid and measuring atomic absorption. Administration of a compound having vitamin D activity or that is metabolized to a compound having vitamin D activity will increase the serum calcium levels. Other non-limiting examples of assays for vitamin D activity include bone mineral density as measured by x-ray absorptiometry (DEXA) or measurement of serum osteocalcin (see U.S. Pat. No. 5,972,917 which is incorporated by reference herein in its entirety).

The dosage of a treatment for vitamin D insufficiency can be determined by a physician and adjusted, as necessary, to suit observed effects of the treatment. With respect to duration and frequency of treatment, it is typical for skilled clinicians to monitor subjects in order to determine when the treatment is providing therapeutic benefit, and to determine whether to increase or decrease dosage, increase or decrease administration frequency, discontinue treatment, resume treatment or make other alteration to treatment regimen.

The dosage ranges for the administration of a treatment for vitamin D insufficiency depend upon the form of the treatment for vitamin D insufficiency, and its potency, as described further herein, and are amounts large enough to produce the desired effect in which the symptoms, markers, or signs of vitamin D insufficiency are reduced. In some embodiments, the symptoms, markers, or signs of vitamin D insufficiency can include the level of bioavailable or free vitamin D determined according to the methods described herein. The dosage should not be so large as to cause substantial adverse side effects. Generally, the dosage can vary with the age, condition, and sex of the patient and can be determined by one of ordinary skill in the art. The dosage can also be adjusted by the individual physician in the event of any complication or based upon the subject's sensitivity to the treatment. By way of non-limiting example, forms of vitamin D or a derivative or analog thereof are typically administered in a therapeutically effective amount of from about 0.1 μg to about 2 mg per day depending upon the compound being administered.

In some embodiments, a vitamin D insufficiency treatment can be administered over a period of time, such as over a 5 minute, 10 minute, 15 minute, 20 minute, or 25 minute period. In some embodiments, the administration can be repeated, for example, on a regular basis, such as hourly for 3 hours, 6 hours, 12 hours or daily or longer or such as biweekly (i.e., every two weeks) for one month, two months, three months, four months or longer. In some embodiments, when multiple doses are administered, the doses can be separated from one another by, for example, six hours, one day, two days, one week, two weeks, one month, or two months.

After an initial treatment regimen, the treatments can be administered on a less frequent basis. For example, after administration biweekly for three months, administration can be repeated once per month, for six months or a year or longer. In some embodiments, administration can be chronic, e.g., one or more doses daily over a period of weeks or months.

Administration of a treatment for vitamin D insufficiency can reduce levels of a marker or symptom of vitamin D insufficiency or a disease or condition associated with vitamin D insufficiency by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80% or at least 90% or more. As used herein, the phrase “therapeutically effective amount”, “effective amount” or “effective dose” refers to an amount that provides a therapeutic benefit in the treatment or management of vitamin D insufficiency. Vitamin D insufficiency can be determined according to the methods described herein and a therapeutically effective amount can be an amount that provides a statistically significant improvement in the level of bioavailable or free vitamin D as determined according to the methods described herein. Determination of a therapeutically effective amount is well within the capability of those of ordinary skill in the art. Generally, a therapeutically effective amount can vary with the subject's history, age, condition, and gender, as well as the severity and type of the medical condition in the subject, and administration of other pharmaceutically active agents.

In some embodiments, the administration is repeated until the level of bioavailable or free vitamin D, as determined according to the methods described herein, no longer indicates that the subject is vitamin D insufficient.

It is to be understood that, for any particular subject, specific dosage regimes should be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions. For example, the dosage of the therapeutic can be increased if the lower dose does not provide sufficient therapeutic activity.

Alternative methods of treating a subject for a vitamin D insufficiency can include, by way of non-limiting example, exposure to sunlight or administration of a CYP24 inhibitor (see U.S. patent application Ser. No. 12/935,139); dentonin peptides (see U.S. patent application Ser. No. 10/360,202); IL-10 or IL-4 polypeptides or TNF-α inhibitors (see U.S. patent application Ser. No. 10/170,746); or PHEX polypeptides as described in U.S. patent application Ser. No. 10/360,202.

With respect to the therapeutic methods of the invention, unless otherwise specified, it is not intended that the administration of the vitamin D insufficiency treatment be limited to a particular mode of administration, dosage, or frequency of dosing; the present invention contemplates all modes of administration, including intramuscular, intravenous, intraperitoneal, intravesicular, intraarticular, topically, subcutaneous, orally or any other route sufficient to provide a dose adequate to treat the vitamin D insufficiency.

Systems

In some aspects, the invention described herein is directed to systems (and computer readable media for causing computer systems) for obtaining data from at least one blood sample obtained from at least one subject, the system comprising 1) a determination module configured to receive the at least one blood sample and perform at least one analysis on the at least one blood sample to determine the level of bioavailable or free vitamin D in the sample; 2) a storage device configured to store data output from the determination module; and 3) a display module for displaying a content based in part on the data output from the determination module, wherein the content comprises a signal indicative of the level of bioavailable or free vitamin D.

In one embodiment, provided herein is a system comprising: (a) at least one memory containing at least one computer program adapted to control the operation of the computer system to implement a method that includes (i) a determination module configured to receive the at least one blood sample and perform at least one analysis on the at least one blood sample to determine the level of bioavailable or free vitamin D in the sample (e.g. determining the level of one or more of VDBP polypeptide, albumin polypeptide, total vitamin D; bioavailable vitamin D; and free vitamin D); (ii) a storage module configured to store output data from the determination module; (iii) a computing module adapted to identify from the output data whether the level of VDBP polypeptide, albumin polypeptide, total vitamin D, bioavailable vitamin D or free vitamin D in a blood sample obtained from a subject indicates that the level of bioavailable or free vitamin D is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects and (iv) a display module for displaying a content based in part on the data output from the determination module, wherein the content comprises a signal indicative of the level of bioavailable or free vitamin D and (b) at least one processor for executing the computer program (see FIG. 6).

The term “computer” can refer to any non-human apparatus that is capable of accepting a structured input, processing the structured input according to prescribed rules, and producing results of the processing as output. Examples of a computer include: a computer; a general purpose computer; a supercomputer; a mainframe; a super mini-computer, a mini-computer; a workstation; a micro-computer; a server; an interactive television; a hybrid combination of a computer and an interactive television; and application-specific hardware to emulate a computer and/or software. A computer can have a single processor or multiple processors, which can operate in parallel and/or not in parallel. A computer also refers to two or more computers connected together via a network for transmitting or receiving information between the computers. An example of such a computer includes a distributed computer system for processing information via computers linked by a network.

The term “computer-readable medium” may refer to any storage device used for storing data accessible by a computer, as well as any other means for providing access to data by a computer. Examples of a storage-device-type computer-readable medium include: a magnetic hard disk; a floppy disk; an optical disk, such as a CD-ROM and a DVD; a magnetic tape; a memory chip.

The term a “computer system” may refer to a system having a computer, where the computer comprises a computer-readable medium embodying software to operate the computer.

The term “software” is used interchangeably herein with “program” and refers to prescribed rules to operate a computer. Examples of software include: software; code segments; instructions; computer programs; and programmed logic.

The computer readable storage media can be any available tangible media that can be accessed by a computer. Computer readable storage media includes volatile and nonvolatile, removable and non-removable tangible media implemented in any method or technology for storage of information such as computer readable instructions, data structures, program modules or other data. Computer readable storage media includes, but is not limited to, RAM (random access memory), ROM (read only memory), EPROM (erasable programmable read only memory), EEPROM (electrically erasable programmable read only memory), flash memory or other memory technology, CD-ROM (compact disc read only memory), DVDs (digital versatile disks) or other optical storage media, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage media, other types of volatile and non-volatile memory, and any other tangible medium which can be used to store the desired information and which can accessed by a computer including and any suitable combination of the foregoing.

Computer-readable data embodied on one or more computer-readable media may define instructions, for example, as part of one or more programs that, as a result of being executed by a computer, instruct the computer to perform one or more of the functions described herein, and/or various embodiments, variations and combinations thereof. Such instructions may be written in any of a plurality of programming languages, for example. Java, J#, Visual Basic, C, C#, C++, Fortran, Pascal, Eiffel, Basic, COBOL assembly language, and the like, or any of a variety of combinations thereof. The computer-readable media on which such instructions are embodied may reside on one or more of the components of either of a system, or a computer readable storage medium described herein, may be distributed across one or more of such components.

The computer-readable media may be transportable such that the instructions stored thereon can be loaded onto any computer resource to implement the aspects of the present invention discussed herein. In addition, it should be appreciated that the instructions stored on the computer-readable medium, described above, are not limited to instructions embodied as part of an application program running on a host computer. Rather, the instructions may be embodied as any type of computer code (e.g., software or microcode) that can be employed to program a computer to implement aspects of the present invention. The computer executable instructions may be written in a suitable computer language or combination of several languages. Basic computational biology methods are known to those of ordinary skill in the art and are described in, for example, Setubal and Meidanis et al., Introduction to Computational Biology Methods (PWS Publishing Company, Boston, 1997); Salzberg, Searles, Kasif, (Ed.), Computational Methods in Molecular Biology, (Elsevier, Amsterdam, 1998); Rashidi and Buehler, Bioinformatics Basics: Application in Biological Science and Medicine (CRC Press, London, 2000) and Ouelette and Bzevanis Bioinformatics: A Practical Guide for Analysis of Gene and Proteins (Wiley & Sons, Inc., 2nd ed., 2001).

Embodiments of the invention can be described through functional modules, which are defined by computer executable instructions recorded on computer readable media and which cause a computer to perform method steps when executed. The modules are segregated by function for the sake of clarity. However, it should be understood that the modules/systems need not correspond to discreet blocks of code and the described functions can be carried out by the execution of various code portions stored on various media and executed at various times. Furthermore, it should be appreciated that the modules can perform other functions, thus the modules are not limited to having any particular functions or set of functions.

The functional modules of certain embodiments of the invention include at minimum a determination module, a storage module, a computing module, and a display module. The functional modules can be executed on one, or multiple, computers, or by using one, or multiple, computer networks. The determination module has computer executable instructions to provide e.g., levels of expression products etc in computer readable form.

The determination module can comprise any system for detecting a signal elicited from an assay to determine the level of any of a VDBP polypeptide, an albumin polypeptide, bioavailable vitamin D, free vitamin D, or total vitamin D as described above herein. In some embodiments, such systems can include an instrument, e.g., AU2700 (Beckman Coulter Brea, Calif.) as described herein for quantitative measurement of polypeptides. In another embodiment, the determination module can comprise multiple units for different functions, such as quantitative measurement of polypeptides (e.g. dye-based photometric assay or quantitative ELISA) and a mass spectroscopy system for the measurement of vitamin D. In one embodiment, the determination module can be configured to perform the methods described elsewhere herein, e.g. dye-based photometric assays for albumin, ELISA assays for VDBP polypeptide levels or mass spectroscopy to determine vitamin D levels. In some embodiments, such systems can include an instrument, e.g., the AU2700 (Beckman Coulter Brea, Calif.).

In some embodiments, the determination system or a further module can be configured to process whole blood samples, e.g. to separate serum from whole blood for use in the assays described herein.

The information determined in the determination system can be read by the storage module. As used herein the “storage module” is intended to include any suitable computing or processing apparatus or other device configured or adapted for storing data or information. Examples of electronic apparatus suitable for use with the present invention include stand-alone computing apparatus, data telecommunications networks, including local area networks (LAN), wide area networks (WAN), Internet, Intranet, and Extranet, and local and distributed computer processing systems. Storage modules also include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage media, magnetic tape, optical storage media such as CD-ROM, DVD, electronic storage media such as RAM, ROM, EPROM, EEPROM and the like, general hard disks and hybrids of these categories such as magnetic/optical storage media. The storage module is adapted or configured for having recorded thereon, for example, sample name, biomolecule assayed and the level of said biomolecule. Such information may be provided in digital form that can be transmitted and read electronically, e.g., via the Internet, on diskette, via USB (universal serial bus) or via any other suitable mode of communication.

As used herein, “stored” refers to a process for encoding information on the storage module. Those skilled in the art can readily adopt any of the presently known methods for recording information on known media to generate manufactures comprising expression level information.

In some embodiments of any of the systems described herein, the storage module stores the output data from the determination module. In additional embodiments, the storage module stores reference information such as levels of bioavailable or free vitamin D in healthy subjects and/or a population of healthy subjects.

The “computing module” can use a variety of available software programs and formats for computing the level of bioavailable or free vitamin D. Such algorithms are well established in the art. A skilled artisan is readily able to determine the appropriate algorithms based on the size and quality of the sample and type of data. The data analysis tools and equations described herein can be implemented in the computing module of the invention. In one embodiment, the computing module further comprises a comparison module, which compares the level of bioavailable or free vitamin D in a blood sample obtained from a subject as described herein with the mean value of bioavailable or free vitamin D in a population of healthy subjects (FIG. 7). By way of an example, when the value of bioavailable vitamin D in a blood sample obtained from a subject is measured, a comparison module can compare or match the output data—with the mean value of bioavailable vitamin D in a population of healthy subjects. In certain embodiments, the mean value of bioavailable or free vitamin D in a population of healthy subjects can be pre-stored in the storage module. During the comparison or matching process, the comparison module can determine whether the level of bioavailable or free vitamin D in the blood sample obtained from a subject is lower than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects. In various embodiments, the comparison module can be configured using existing commercially-available or freely-available software for comparison purpose, and may be optimized for particular data comparisons that are conducted.

The computing and/or comparison module, or any other module of the invention, can include an operating system (e.g., UNIX) on which runs a relational database management system, a World Wide Web application, and a World Wide Web server. World Wide Web application includes the executable code necessary for generation of database language statements (e.g., Structured Query Language (SQL) statements). Generally, the executables will include embedded SQL statements. In addition, the World Wide Web application may include a configuration file which contains pointers and addresses to the various software entities that comprise the server as well as the various external and internal databases which must be accessed to service user requests. The Configuration file also directs requests for server resources to the appropriate hardware—as may be necessary should the server be distributed over two or more separate computers. In one embodiment, the World Wide Web server supports a TCP/IP protocol. Local networks such as this are sometimes referred to as “Intranets.” An advantage of such Intranets is that they allow easy communication with public domain databases residing on the World Wide Web (e.g., the GenBank or Swiss Pro World Wide Web site). In some embodiments users can directly access data (via Hypertext links for example) residing on Internet databases using a HTML interface provided by Web browsers and Web servers (FIG. 8).

The computing and/or comparison module provides a computer readable comparison result that can be processed in computer readable form by predefined criteria, or criteria defined by a user, to provide content based in part on the comparison result that may be stored and output as requested by a user using an output module, e.g., a display module.

In some embodiments, the content displayed on the display module can be the level of bioavailable or free vitamin D in the blood sample obtained from a subject. In some embodiments, the content displayed on the display module can be the relative level of bioavailable or free vitamin D in the blood sample obtained from a subject as compared to the mean level of bioavailable or free vitamin D in a population of healthy subjects. In some embodiments, the content displayed on the display module can indicate whether the level of bioavailable or free vitamin D in the blood sample obtained from a subject is less or more than a threshold level, e.g., the 25th percentile value or 25% of the mean value, of bioavailable or free vitamin D in a population of healthy subjects. In some embodiments, the content displayed on the display module can indicate whether the subject has an insufficient level of vitamin D. In some embodiments, the content displayed on the display module can indicate whether the subject is in need of a treatment for vitamin D insufficiency. In some embodiments, the content displayed on the display module can indicate whether the subject has an increased risk or likelihood of having or developing a vitamin D-associated disease. In some embodiments, the content displayed on the display module can be a numerical value indicating one of these risks or probabilities. In such embodiments, the probability can be expressed in percentages or a fraction. For example, higher percentage or a fraction closer to 1 indicates a higher likelihood of a subject having a vitamin D-associated disease. In some embodiments, the content displayed on the display module can be single word or phrases to qualitatively indicate a risk or probability. For example, a word “unlikely” can be used to indicate a lower risk for having or developing a vitamin D-associated disease, while “likely” can be used to indicate a high risk for having or developing a vitamin D-associated disease.

In one embodiment of the invention, the content based on the computing and/or comparison result is displayed on a computer monitor. In one embodiment of the invention, the content based on the computing and/or comparison result is displayed through printable media. The display module can be any suitable device configured to receive from a computer and display computer readable information to a user. Non-limiting examples include, for example, general-purpose computers such as those based on Intel PENTIUM-type processor, Motorola PowerPC, Sun UltraSPARC, Hewlett-Packard PA-RISC processors, any of a variety of processors available from Advanced Micro Devices (AMD) of Sunnyvale, Calif., or any other type of processor, visual display devices such as flat panel displays, cathode ray tubes and the like, as well as computer printers of various types.

In one embodiment, a World Wide Web browser is used for providing a user interface for display of the content based on the computing/comparison result. It should be understood that other modules of the invention can be adapted to have a web browser interface. Through the Web browser, a user can construct requests for retrieving data from the computing/comparison module. Thus, the user will typically point and click to user interface elements such as buttons, pull down menus, scroll bars and the like conventionally employed in graphical user interfaces.

In some embodiments, the system further comprises a means of inputting a value for the level of one or more of VDBP polypeptide, albumin polypeptide, and total vitamin D determined to be in a blood sample obtained from a subject. By way of non-limiting example, the level of albumin polypeptide can be determined by the determination module of the system while the level of VDBP polypeptide is determined by an ELISA assay performed separately from the system described herein. When the level of VDBP polypeptide is determined, the value for this level can be entered into the computing module of the system and used to determine the level of bioavailable or free vitamin D in the blood sample obtained from the subject. In some embodiments, the inputting means comprises a keyboard or touchscreen which allows a user to type a value which is accepted by the computing module.

Systems and computer readable media described herein are merely illustrative embodiments of the invention for determining the level of bioavailable or free vitamin D in a blood sample obtained from a subject, and therefore are not intended to limit the scope of the invention. Variations of the systems and computer readable media described herein are possible and are intended to fall within the scope of the invention.

The modules of the machine, or those used in the computer readable medium, may assume numerous configurations. For example, function may be provided on a single machine or distributed over multiple machines.

The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments can perform functions in a different order, or functions can be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. These and other changes can be made to the disclosure in light of the detailed description.

Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments can also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.

All patents and other publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.

Some embodiments of the present invention can be defined as any of the following numbered paragraphs:

-   -   1. An assay comprising:         -   analyzing a blood sample obtained from a subject to             determine a level of VDBP (vitamin D binding protein)             polypeptide, albumin polypeptide and total vitamin D;         -   wherein a level of bioavailable vitamin D is:             =(K _(alb)*[Alb]+1)*[Free Vitamin D]         -   and wherein a level of free vitamin D is:             ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K             _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total             Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K             _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K             _(DBP)})     -   1a. A differential affinity precipitation assay performed by a         method comprising:         -   contacting a sample comprising serum or plasma from a             subject with purified Vitamin D Binding Polypeptide (VDBP),             wherein the purified VDBP is immobilized on a substrate             (e.g., beads, solid surface) for a time sufficient for free             and albumin-bound Vitamin D in the sample to bind to the             purified VDBP, thereby forming a test sample comprising             Vitamin D-VDBP complexes;             -   optionally removing any Vitamin D not bound to the                 purified VDBP from the test sample; contacting the                 Vitamin D-VDBP complexes with a known amount of free                 labeled Vitamin D, for a time sufficient for the labeled                 Vitamin D to equilibrate with the Vitamin D-VDBP                 complexes in the test sample; and preferably removing                 any labeled Vitamin D from the sample that is not bound                 to the VDBP;         -   determining the amount of labeled Vitamin D bound to the             purified VDBP in the test sample, and calculating the amount             of bioavailable Vitamin D in the sample from the subject             based on the amount of labeled Vitamin D bound to the             purified VDBP in the test sample.     -   2. The assay of paragraphs 1 or 1a, wherein a level of         bioavailable vitamin D lower than a threshold level, e.g., the         25th percentile value or 25% of the mean value, of bioavailable         vitamin D in a population of healthy subjects indicates that the         subject has a vitamin D insufficiency.     -   3. The assay of any of paragraphs 1-2, wherein the vitamin D is         selected from the group consisting of:         -   25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.     -   4. The assay of any of paragraphs 1-3, wherein the determining         of the level of VDBP polypeptide or albumin polypeptide         comprises use of a method selected from the group consisting of:         -   enzyme linked immunosorbent assay; chemiluminescent             immunosorbent assay; electrochemiluminescent immunosorbent             assay; fluorescent immunosorbent assay; dye linked             immunosorbent assay; immunoturbidimetric assay;             immunonephelometric assay; dye-based photometric assay;             western blot; immunoprecipitation; radioimmunological assay             (RIA); radioimmunometric assay; immunofluorescence assay and             mass spectroscopy.     -   5. The assay of any of paragraphs 1-4, wherein the determining         of the level of total vitamin D comprises the use of a method         selected from the group consisting of:         -   radioimmunoassay; liquid chromatography tandem mass             spectroscopy; enzyme linked immunosorbent assay;             chemiluminescent immunosorbent assay;             electrochemiluminescent immunosorbent assay; fluorescent             immunosorbent assay; and high-pressure liquid             chromatography.     -   6. The assay of any of paragraphs 1-5, wherein an insufficiency         of vitamin D indicates an increased risk of a condition selected         from the group consisting of:         -   decreased bone density; decreased bone mineral density; bone             fractures; bone resorption; rickets; osteitis fibrosa             cystica; fibrogenesis imperfect ossium; osteosclerosis;             osteoporosis; osteomalacia; elevated parathyroid hormone             levels; parathyroid gland hyperplasia secondary             hyperparathyroidism; hypocalcemia; infection; cancer;             psoriasis; cardiovascular disease; renal osteodystrophy;             renal disease; end-stage renal disease; chronic kidney             disease; chronic kidney disease-associated mineral and bone             disorder; extraskeletal calcification; obesity; allergy,             asthama; multiple sclerosis; muscle weakness; rheumatoid             arthritis and diabetes.     -   7. The assay of any of paragraphs 1-6, further comprising the         step of administering a vitamin D insufficiency treatment to a         subject who is determined to have a vitamin D insufficiency.     -   8. The assay of any of paragraphs 1-7, wherein the treatment         comprises administering a compound selected from the group         consisting of:         -   calcitriol; dihydrotachysterol; doxercalciferol;             paricalcitol; cholecalciferol and ergocalciferol.     -   9. An assay comprising:         -   analyzing a blood sample obtained from a subject to             determine a level of VDBP polypeptide, albumin polypeptide             and total vitamin D;         -   wherein a level of free vitamin D is:             ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K             _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total             Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K             _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K             _(DBP)})     -   10. The assay of paragraph 9, wherein a level of free vitamin D         lower than a threshold level, e.g., the 25th percentile value or         25% of the mean value, of free vitamin D in a population of         healthy subjects indicates that the subject has a vitamin D         insufficiency.     -   11. The assay of any of paragraphs 9-10, wherein the vitamin D         is selected from the group consisting of:         -   25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.     -   12. The assay of any of paragraphs 9-11, wherein the determining         of the level of VDBP polypeptide or albumin polypeptide         comprises the use of a method selected from the group consisting         of:         -   enzyme linked immunosorbent assay; chemiluminescent             immunosorbent assay; electrochemiluminescent immunosorbent             assay; fluorescent immunosorbent assay; dye linked             immunosorbent assay; immunoturbidimetric assay;             immunonephelometric assay; dye-based photometric assay;             western blot; immunoprecipitation; radioimmunological assay             (RIA); radioimmunometric assay; immunofluorescence assay and             mass spectroscopy.     -   13. The assay of any of paragraphs 9-12, wherein the determining         of the level of total vitamin D comprises the use of a method         selected from the group consisting of:         -   radioimmunoassay; liquid chromatography tandem mass             spectroscopy; enzyme linked immunosorbent assay;             chemiluminescent immunosorbent assay;             electrochemiluminescent immunosorbent assay; fluorescent             immunosorbent assay; and high-pressure liquid             chromatography.     -   14. The assay of any of paragraphs 9-13, wherein an         insufficiency of vitamin D indicates an increased risk of a         condition selected from the group consisting of:         -   decreased bone density; decreased bone mineral density; bone             fractures; bone resorption; rickets; osteitis fibrosa             cystica; fibrogenesis imperfect ossium; osteosclerosis;             osteoporosis; osteomalacia; elevated parathyroid hormone             levels; parathyroid gland hyperplasia; secondary             hyperparathyroidism; hypocalcemia; infection; cancer;             psoriasis; cardiovascular disease; renal osteodystrophy;             renal disease; end-stage renal disease; chronic kidney             disease; chronic kidney disease-associated mineral and bone             disorder; extraskeletal calcification; obesity; allergy,             asthama; multiple sclerosis; muscle weakness; rheumatoid             arthritis and diabetes.     -   15. The assay of any of paragraphs 9-14, further comprising the         step of administering a vitamin D insufficiency treatment to a         subject who is determined to have a vitamin D insufficiency.     -   16. The assay of any of paragraphs 9-15, wherein the treatment         comprises administering a compound selected from the group         consisting of:         -   calcitriol; dihydrotachysterol; doxercalciferol;             paricalcitol; cholecalciferol and ergocalciferol.     -   17. A method for treating a vitamin D insufficiency in a subject         comprising detecting a level of VDBP polypeptide, albumin         polypeptide and total vitamin D in a blood sample obtained from         a subject;         -   wherein a level of bioavailable vitamin D is:             =(K _(alb)*[Alb]+1)*[Free Vitamin D]         -   and wherein a level of free vitamin D is:             ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K             _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total             Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K             _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K             _(DBP)}).         -   and administering a treatment for vitamin D insufficiency to             the subject if the level of bioavailable vitamin D is less             than a threshold level, e.g., the 25th percentile value or             25% of the mean value, of the mean value of bioavailable             vitamin D in a population of healthy subjects.     -   18. A method for treating a vitamin D insufficiency in a subject         comprising detecting a level of VDBP polypeptide, albumin         polypeptide and total vitamin D in a blood sample obtained from         a subject;         -   wherein a level of free vitamin D is:             ={−{K _(DBP)·[Total DBP]−K _(DBP)·[Total Vitamin D]+K             _(alb)·[Alb]+1}+√{(K _(DBP)·[Total DBP]−K _(DBP)·[Total             Vitamin D]+K _(alb)·[Alb]+1)²+4·(K _(DBP) ·K _(alb)·[Alb]+K             _(DBP))·([Total Vitamin D])}}÷(2·{K _(DBP) ·K _(alb)·[Alb]+K             _(DBP)})         -   and administering a treatment for vitamin D insufficiency to             the subject if the level of free vitamin D is less than a             threshold level, e.g., the 25th percentile value or 25% of             the mean value, of free vitamin D in a population of healthy             subjects.     -   18a. A method for treating a vitamin D insufficiency in a         subject comprising a level of bioavailable vitamin D in a blood         sample obtained from a subject; wherein a level of bioavailable         vitamin D is determined using a method comprising:         -   contacting a sample comprising serum or plasma from a             subject with purified Vitamin D Binding Polypeptide (VDBP),             wherein the purified VDBP is immobilized on a substrate             (e.g., beads, solid surface) for a time sufficient for free             and albumin-bound Vitamin D in the sample to bind to the             purified VDBP, thereby forming a test sample comprising             Vitamin D-VDBP complexes;         -   optionally removing any Vitamin D not bound to the purified             VDBP from the test sample;         -   contacting the Vitamin D-VDBP complexes with a known amount             of free labeled Vitamin D, for a time sufficient for the             labeled Vitamin D to equilibrate with the Vitamin D-VDBP             complexes in the test sample; and preferably removing any             labeled Vitamin D from the sample that is not bound to the             VDBP;         -   determining the amount of labeled Vitamin D bound to the             purified VDBP in the test sample, and calculating the amount             of bioavailable Vitamin D in the sample from the subject             based on the amount of labeled Vitamin D bound to the             purified VDBP in the test sample,         -   and administering a treatment for vitamin D insufficiency to             the subject if the level of free vitamin D is below a             threshold level, e.g., the 25th percentile value or 25% of             the mean value, of the mean value of free vitamin D in a             population of healthy subjects.     -   19. A system for obtaining data from at least one blood sample         obtained from at least one subject, the system comprising:         -   a determination module configured to receive the at least             one blood sample and perform at least one analysis on the at             least one blood sample to determine a level of bioavailable             or free vitamin D in the sample;         -   a storage device configured to store data output from said             determination module; and         -   a display module for displaying a content based in part on             the data output from said determination module, wherein the             content comprises a signal indicative of the level of             bioavailable or free vitamin D.     -   20. The system of paragraph 19, wherein the system further         comprises a means of inputting a value for the level of one or         more of VDBP polypeptide, albumin polypeptide, and total vitamin         D determined to be in a test sample.     -   21. The system of any of paragraphs 19-20, wherein the content         displayed on said display module further comprises a signal         indicative of the subject having an increased likelihood of a         vitamin D insufficiency if the level of bioavailable or free         vitamin D is determined to be lower than a threshold level,         e.g., the 25th percentile value or 25% of the mean value, of         bioavailable vitamin D in a population of healthy subjects.     -   22. The system of any of paragraphs 19-21, wherein the content         displayed on said display module further comprises a signal         indicative of the subject being recommended to receive a         treatment for vitamin D insufficiency.     -   23. A method of treatment comprising:         -   analyzing a blood sample obtained from a subject to             determine a level of free or bioavailable vitamin D;         -   wherein a level of free or bioavailable vitamin D lower than             a threshold level, e.g., the 25th percentile value or 25% of             the mean value, of free or bioavailable vitamin D in a             population of healthy subjects indicates that the subject             has a vitamin D insufficiency; and         -   administering a vitamin D insufficiency treatment to a             subject who is determined to have a vitamin D insufficiency.     -   24. The method of paragraph 23, wherein the vitamin D is         selected from the group consisting of:         -   25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.     -   25. The method of any of paragraphs 23-24, wherein the         determining of the level of free or bioavailable vitamin D         comprises use of a method selected from the group consisting of:         -   immunoassay; two-step immunoassay with antibody capture;             one-step immunoassay with immobilized antibody and             competitive detection; one-step immunoassay with immobilized             competitor and labeled antibody; fluorescence polarization             immunoassay; differential precipitation             (immunoprecipitation, affinity precipitation);             immunodepletion; and affinity binding chromatography;         -   and a method selected from the group consisting of:         -   radioimmunoassay; chemiluminescent immunosorbent assay;             electrochemiluminescent immunosorbent assay; fluorescent             immunosorbent assay; dye linked immunosorbent assay; liquid             chromatography tandem mass spectroscopy and high-pressure             liquid chromatography.     -   26. The method of any of paragraphs 23-25, wherein an         insufficiency of vitamin D indicates an increased risk of a         condition selected from the group consisting of:         -   decreased bone density; decreased bone mineral density; bone             fractures; bone resorption; rickets; osteitis fibrosa             cystica; fibrogenesis imperfect ossium; osteosclerosis;             osteoporosis; osteomalacia; elevated parathyroid hormone             levels; parathyroid gland hyperplasia; secondary             hyperparathyroidism; hypocalcemia; infection; cancer;             psoriasis; cardiovascular disease; renal osteodystrophy;             renal disease; end-stage renal disease; chronic kidney             disease; chronic kidney disease-associated mineral and bone             disorder, extraskeletal calcification; obesity; allergy,             asthama; multiple sclerosis; muscle weakness; rheumatoid             arthritis and diabetes.     -   27. The method of any of paragraphs 23-26, wherein the treatment         comprises administering a compound selected from the group         consisting of:         -   calcitriol; dihydrotachysterol; doxercalciferol;             paricalcitol; cholecalciferol and ergocalciferol.     -   28. An assay comprising:         -   analyzing a blood sample obtained from a subject to             determine a level of free vitamin D and albumin polypeptide;         -   wherein a level of bioavailable vitamin D is:             =(K _(alb)*[Alb]+1)*[Free Vitamin D]     -   29. The assay of paragraph 28, wherein a level of bioavailable         vitamin D lower than a threshold level, e.g., the 25th         percentile value or 25% of the mean value, of bioavailable         vitamin D in a population of healthy subjects indicates that the         subject has a vitamin D insufficiency.     -   30. The assay of any of paragraphs 28-29, wherein the vitamin D         is selected from the group consisting of:         -   25-hydroxyvitamin D and 1,25-dihydroxyvitamin D.     -   31. The assay of any of paragraphs 28-30, wherein the         determining of the level of albumin polypeptide comprises use of         a method selected from the group consisting of:         -   enzyme linked immunosorbent assay; chemiluminescent             immunosorbent assay; electrochemiluminescent immunosorbent             assay; fluorescent immunosorbent assay; dye linked             immunosorbent assay; immunoturbidimetric assay;             immunonephelometric assay; dye-based photometric assay;             western blot; immunoprecipitation; radioimmunological assay             (RIA); radioimmunometric assay; immunofluorescence assay and             mass spectroscopy.     -   32. The assay of any of paragraphs 28-31, wherein the         determining of the level of free vitamin D comprises the use of         a method selected from the group consisting of:         -   immunoassay; two-step immunoassay with antibody capture;             one-step immunoassay with immobilized antibody and             competitive detection; one-step immunoassay with immobilized             competitor and labeled antibody; fluorescence polarization             immunoassay; differential precipitation             (immunoprecipitation, affinity precipitation);             immunodepletion; and affinity binding chromatography;         -   and a method selected from the group consisting of:         -   radioimmunoassay; chemiluminescent immunosorbent assay;             electrochemiluminescent immunosorbent assay; fluorescent             immunosorbent assay; liquid chromatography tandem mass             spectroscopy and high-pressure liquid chromatography.     -   33. The assay of any of paragraphs 28-32, wherein an         insufficiency of vitamin D indicates an increased risk of a         condition selected from the group consisting of:         -   decreased bone density; decreased bone mineral density; bone             fractures; bone resorption; rickets; osteitis fibrosa             cystica; fibrogenesis imperfect ossium; osteosclerosis;             osteoporosis; osteomalacia; elevated parathyroid hormone             levels; parathyroid gland hyperplasia; secondary             hyperparathyroidism; hypocalcemia; infection; cancer;             psoriasis; cardiovascular disease; renal osteodystrophy;             renal disease; end-stage renal disease; chronic kidney             disease; chronic kidney disease-associated mineral and bone             disorder; extraskeletal calcification; obesity; allergy,             asthama; multiple sclerosis; muscle weakness; rheumatoid             arthritis and diabetes.     -   34. The assay of any of paragraphs 28-33, further comprising the         step of administering a vitamin D insufficiency treatment to a         subject who is determined to have a vitamin D insufficiency.     -   35. The assay of any of paragraphs 28-34, wherein the treatment         comprises administering a compound selected from the group         consisting of:         -   calcitriol; dihydrotachysterol; doxercalciferol;             paricalcitol; cholecalciferol and ergocalciferol.

EXAMPLES

This invention is further illustrated by the following examples which should not be construed as limiting.

Example 1: Bioavailable Vitamin D and Bone Mineral Density

Studies examining the relationship between total circulating 25-hydroxyvitamin D (25(OH)D) levels and bone mineral density (BMD) have yielded mixed results. Vitamin D binding protein (DBP), the major carrier protein for 25(OH)D, may alter the biologic activity of circulating vitamin D. Demonstrated herein is a test of the hypothesis that free and bioavailable 25(OH)D, calculated from total 25(OH)D, DBP and serum albumin levels, is more strongly associated with BMD than levels of total 25(OH)D.

Total 25(OH)D, DBP, and serum albumin levels were measured in 49 healthy young adults enrolled in the Metabolic Abnormalities in College-Aged Students (MACS) study. Lumbar spine BMD was measured in all subjects using dual X-ray absorptiometry. Clinical, diet, and laboratory information was also gathered at this time. Free and bioavailable (free+albumin bound) 25(OH)D was determined and their associations with BMD were examined.

BMD was not associated with total 25(OH)D levels (r=0.172 p=0.236). In contrast, free and bioavailable 25(OH)D levels and the ratio of total 25(OH)D concentrations divided by VDBP concentrations (referred to herein as the Vitamin D Index) were positively correlated with BMD (r=0.413 p=0.003 for free, r=0.441 p=0.002 for bioavailable, r=0.406 p=0.003). Bioavailable 25(OH)D levels remained independently associated with BMD in multivariate regression models adjusting for age, sex, body mass index, and race (p=0.03). Free and bioavailable 25(OH)D are more strongly correlated with BMD than total 25(OH)D. These findings have important implications for vitamin D supplementation in vitamin D deficient states.

Introduction

Vitamin D insufficiency is associated with decreased calcium absorption and elevated levels of parathyroid hormone (PTH),(1) which may lead to excessive bone resorption.(2) In some observational studies, higher levels of 25-hydroxyvitamin D (25(OH)D) have been linked to increased bone mineral density (BMD) and decreased risk of fracture.(3-7) Additionally, several randomized control trials suggest that vitamin D supplementation reduces the risk of fracture and increases BMD.(8-14) However, not all observational studies have confirmed the relationship between 25-hydroxyvitamin D (25(OH)D) and BMD, especially in younger populations or racial minorities.(15-19) Moreover, in several randomized trials, the effect of vitamin D supplementation on BMD or fracture risk has been modest,(8) absent,(20-22) or reversed.(23)

The free hormone hypothesis postulates that only hormones liberated from binding proteins enter cells and produce biological action.(24) 25(OH)D and 1,25-dihydroxyvitamin D (1,25(OH)2D) circulate bound to vitamin D binding protein (85-90%) and albumin (10-15%) with less than 1% of circulating hormone in its free form.(25) In mice, vitamin D binding protein (DBP) prolongs the serum half life of 25(OH)D and protects against vitamin D insufficiency by serving as a vitamin D reservoir.(26) However, DBP also limits the biological activity of injected 1,2 (OH)2D in mice(26) and inhibits the action of vitamin D on monocytes and keratinocytes in vitro.(27-28). The significance of circulating DBP levels with regards to vitamin D's biological action in humans is unclear.

The free fraction of 25(OH)D and the binding affinity constants for 25(OH)D's interaction with DBP and albumin have previously been measured.(29) Formulae for the calculation of free 25(OH)D levels based on serum concentrations of total 25(OH)D, DBP, albumin, and have been developed based on this data. Measured and calculated values of free 25(OH)D are highly correlated.(29)

Materials and Methods

Subject Recruitment.

A cross-sectional study was conducted in a subset of healthy young adults enrolled in the Metabolic Abnormalities in College Students study (MACS), a study designed to evaluate the prevalence of metabolic abnormalities in university students.(30) Subjects were healthy 18-31 year old male and female students from private universities in the Boston area. 170 subjects were recruited through flyers posted throughout the Massachusetts Institute of Technology (MIT) campus and through targeted emails to random members of the student population. All subjects provided written informed consent. The study was approved by the MIT Committee on the Use of Humans as Experimental Subjects. 49 subjects had sufficient sample for inclusion in this analysis and their characteristics are presented in Table 1.

Study Visit.

Subjects were instructed to fast for 12 hours prior to admission to the MIT Clinical Research Center as outpatients and underwent a baseline evaluation including a blood sample collection and various physiologic measurements. Structured interviews were conducted by study nurses to collect standard clinical information, minutes of exercise per week (in 30 minute increments), and medication/supplement use. Height was measured using a standing stadiometer (Holton Ltd, Crymych, Dyfed, UK). Weight was measured using a calibrated scale (SECA, Hanover, Md., USA). Body mass index (BMI) was calculated as weight(kg)/[height(m)].

Dietary Information.

Subjects completed a written food record 1 week prior to the day of study, recording 4 full days of food intake, including one weekend day. During the study visit to the MIT CRC, a registered dietitian reviewed the food record with the subject to clarify the quantities and sources of food consumed. Dietary intake data were then analyzed using Nutrition Data System for Research software version 2006/2007 (Nutrition Coordinating Center, University of Minnesota. Minneapolis, Minn.).

Bone Density Measurement.

Subjects underwent total-body dual-energy x-ray absorptiometry (DEXA) (Hologic QDR-4500A; Hologic. Waltham, Mass., USA) to determine total and regional BMD.(31) Hologic phantoms were used to calibrate the instrument. Lumbar spine BMD was used in this study as the measure of BMD. Lumbar spine BMD is a preferred site for the diagnosis of osteoporosis and the prediction of fracture. No hip BMD measurements were available. (32-33)

Biochemical Analysis.

Baseline blood samples were frozen at −80° C. and stored for later analysis. 25(OH)D, serum calcium, albumin, and levels of PTH were measured in the Massachusetts General Hospital (MGH) clinical laboratories. 25(OH)D2 and 25(OH)D3 levels were measured by liquid chromatography tandem mass spectrometry (LC-MS), with interassay CV's of 9.1% for 25(OH)D₂ and 8.6% for 25(OH)D₃. Total 25(OH)D level was calculated as the sum of 25(OH)D₂ level and 25(OH)D₃ level. Intact PTH was measured by electrochemiluminescense immunoassay on the Cobas E160 automated analyzer (Roche Diagnostics, Indianapolis, Ind.). Interassay CV for intact PTH measurement was 4.2%. Calcium and albumin levels were measured by dye-based photometric assays on an automated analyzer. DBP was measured in duplicate by commercial enzyme linked immunosorbent assay (ELISA) (R&D Systems, Minneapolis, Minn., Catalog Number DVDBP0) according to the manufacturer's instructions. The assay was conducted after diluting serum samples 1 to 2,000 in Calibrator Diluent RD6-11 (R&D Systems Part Number 895489). Inter-assay CV was 8.5% at a concentration of 40 ug/ml. The assay recovered between 93 and 110% of a 100-200 ug/mL dose of exogenous vitamin D binding protein added to human serum samples containing between 25-200 ug/mL of endogenous vitamin D binding protein. The manufacturer reports no significant cross-reactivity with human albumin, vitamin D3, or alpha-fetoprotein. In a subset of patients in whom adequate serum was available (N=45), total 1,25(OH)₂D was measured by LC-MS/MS in the Mayo Clinic Medical Laboratories (Rochester, Minn., USA).

Calculation of Unbound 25(OH)D.

Free levels of 25(OH)D were calculated using two methods. Both methods used the binding affinity constants between albumin and DBP and 25(OH)D measured in a previous study which used centrifugal ultrafiltration to determine the free fraction of 25(OH)D.(29)

Method 1:

Free levels of 25(OH)D were calculated using the following equation:

${{Free}\mspace{14mu} 25({OH})D} = {\frac{{Total}\mspace{14mu} 25({OH})D}{1 + \left( {6 \times 10^{5} \times {Albumin}} \right) + \left( {7 \times 10^{8} \times {DBP}} \right)}.}$ (29) The reported correlation coefficient between calculated free 25(OH)D using this equation and measured free 25(OH)D by centrifugal ultrafiltration is 0.925.(29) Free 1,25(OH)D levels were also calculated using this method.(25)

Method 2:

Free, bioavailable, and DBP-bound 25(OH)D were calculated using equations described in Appendix 1 of this Example below. These methods define bioavailable hormone as the fraction that is both free and albumin-bound, i.e. the fraction not bound to circulating binding proteins such as DBP.

Both calculation methods used the same affinity binding constants. Applied to the same measurements of total 25(OH)D, DBP, and albumin, they produce calculated free 25(OH)D values that are highly correlated (Spearman r=1), however the equations produce values that are an average of 1.4% higher (data not shown). Because the equations also provide for separate calculation of free, bioavailable, and DBP-bound 25(OH)D, Method 2 procedures were used for subsequent analyses of 25(OH)D levels.

Statistical Analysis.

Subject characteristics are reported as mean±SD unless otherwise noted. Non-normal variables including 25(OH)D levels, DBP levels, BMD, and dietary calcium intake levels showed skewed distributions and were natural log transformed in order to meet the assumptions of parametric statistical techniques. Exercise amount was dichotomized at 120 minutes per week. Pearson's correlation coefficients were calculated to assess the relationships between 25(OH)D levels, BMD, and other continuous variables. Independent samples t-tests were used to compare 25(OH)D levels, DBP levels, and BMD among subgroups defined by race, sex, exercise amount, and oral contraceptive use. Linear regression analysis was used to test for the presence of an independent relationship between 25(OH)D levels, DBP, and BMD after adjustment for factors previously reported to be associated with bone density including age, sex, BMI and race. (5,8,12,35-36) All analyses were conducted using STATA Statistical Software (College Station, Tex.) version 11. Two sided p-values <0.05 were considered statistically significant.

Results

Subject characteristics are shown in Table 1. There was wide variation in levels of DBP, with concentrations ranging from 0.66 to 11.2 umol/L. Accordingly, calculated free and bioavailable 25(OH)D levels ranged widely (Table 2). Total 25-hydroxyvitamin D levels were positively correlated with DBP levels (r=0.335, p=0.019).

Total 25(OH)D levels were not correlated with BMD (r=−0.172 p=0.236, FIG. 1). Similarly, levels of DBP-bound 25(OH)D were not correlated with BMD (r-=0.072, p=0.626). In contrast, free and bioavailable 25(OH)D levels and Vitamin D index values were all strongly correlated with BMD (r=0.413 p=0.003 for free, r=0.441 p=0.002 for bioavailable, and r=0.406 p=0.003 for Vitamin D Index values, FIG. 1). Bioavailable and free 25(OH)D levels were highly correlated with each other (r=0.985, p<0.001), but bioavailable 25(OH)D made up a larger portion of the total 25(OH)D with approximately 350-fold higher concentrations of bioavailable 25(OH)D compared to free 25(OH)D. (Table 2) Total and calculated free levels of 1,25(OH)₂D were not correlated with BMD (p>0.05). Total levels of 1,25(OH)₂D were not associated with free or bioavailable 25(OH)D levels (p>0.05), nor was sex-adjusted alkaline phosphatase associated with total, free, or bioavailable 25(OH) D (p>0.05) Neither total nor bioavailable 25(OH)D levels were correlated with serum calcium or PTH levels (p>0.05). Of note, PTH levels fell between 15 and 51 ng/L (all within the normal range) and were not associated with BMD (r=−0.024, p=0.869).

Both total 25(OH)D and DBP levels were inversely associated with BMI (r=−0.300, p=0.036 for total and r=−0.542, p<0.001 for DBP). Bioavailable 25(OH)D was positively correlated with BMI (r=0.302, p=0.035). However, in this population, BMI was not correlated with BMD (r=0.160, p=0.271). Dietary calcium intake was correlated with total 25(OH)D (r=0.339, p=0.021), but was not correlated with DBP, bioavailable 25(OH)D, or BMD (p>0.05). Levels of total and bioavailable 25(OH)D, DBP and BMD among selected subgroups are shown in Table 3. Females had greater average total 25(OH)D levels than males, but average DBP levels, bioavailable 25(OH)D levels and BMD did not differ between males and females. Females reporting use of oral contraceptive pills (OCP) had higher average total 25(OH)D compared with females who did not report OCP use, but average DBP and bioavailable 25(OH)D levels were not significantly different based on OCP use. Subjects with BMI greater than or equal to 25 kg/m² (overweight subjects) had lower DBP levels than subjects with BMI less than 25 kg/m² (normal weight subjects). Subjects who reported exercising 120 minutes a week or more had higher average total 25(OH)D levels than subjects who did not, but no significant difference was found in average DBP levels, bioavailable 25(OH)D levels, and BMD. Average DBP levels in non-white subjects were lower than in white subjects (Table 3).

In multivariate models adjusting for age, sex, BMI and race, bioavailable 25(OH)D remained independently associated with BMD (p=0.03, Table 4). Bioavailable 25(OH)D was the only significant predictor of BMD in multivariate models. As the level of calculated bioavailable 25(OH)D is dependent on the concentrations of total 25(OH)D, albumin, and DBP, it was separately assessed whether albumin or DBP was associated with BMD. DBP level was inversely correlated with BMD (r=−0.296, p=0.039) while serum albumin showed no association with BMD (r=0.156, p=0.285). In a multivariate linear regression model, total 25(OH)D became a significant predictor of BMD only after adjustment for DBP level (B=0.089, p=0.040). Albumin was not associated with BMD in a multivariate model including DBP and total 25(OH)D (p=0.150).

Discussion

In light of conflicting reports concerning the relationship between circulating levels of 25(OH)D and BMD, serum levels of total 25(OH)D, DBP, and albumin were measured in a group of young healthy adults and assessed relationships between free 25(OH)D, bioavailable 25(OH)D, total 25(OH)D and BMD. Without meaning to be limiting, the results described herein are consistent with the free hormone hypothesis and suggest that circulating DBP is an inhibitor of the biological action of vitamin D in humans. The similar associations between free and bioavailable vitamin levels and BMD imply that, unlike binding to DBP, binding to albumin does not inhibit the action of 25(OH)D. These results are consistent with prior basic and clinical studies on DBP.

The results described herein support the hypothesis that DBP behaves similarly to other serum hormone carrier proteins and have broad clinical applications. Like thyroid hormone binding globulin and sex hormone binding globulin, DBP may act as a serum carrier and reservoir, prolonging the circulating half-life of vitamin D, while at the same time regulating its immediate bioavailability to target tissues.(24). In contrast to the megalin-mediated endocytosis described in renal tubular cells, our results imply that 25(OH)D gains access to some target cells by diffusion across cell membranes, similar to these other steroid hormones.(24) Thus hormonal activity and sufficiency may be reflected by the amounts of bioavailable vitamin, not by total serum levels. Currently, clinical testing for vitamin D insufficiency is based upon measurement of total serum concentrations of 25(OH)D.(2) Yet, the data described herein suggests that concentrations of total serum vitamin D may not be the best measure of vitamin D sufficiency. For example, patients with high levels of DBP may appear to be 25(OH)D sufficient, but may actually be deficient in bioavailable vitamin. Conversely, in patients with low levels of DBP, total 25(OH)D will be low, but these patients may actually have sufficient bioavailable vitamin. The maintenance of bioavailable 25(OH)D levels in obese and non-white subjects, despite lower levels of total 25(OH)D raise the possibility that variation in circulating DBP explains the apparent paradox of low 25(OH)D levels and higher BMD in black and overweight patients seen in several previous studies, (5,15-16,35,44-45).

The results described herein contrast with results of some prior studies linking total 25(OH)D levels to BMD, but are consistent with other studies which failed to find such a relationship.(4-5,15-18) In these prior studies, DBP levels were not measured. Of note, total 25(OH)D and free/bioavailable 25(OH)D levels are associated, and it is possible that a larger sample size would have enabled detection of a weak relationship between total 25(OH)D and BMD. Prior studies that found this relationship generally had sample sizes greater than 200 and when correlation coefficients between 25(OH)D and BMD were reported, they were less than 0.2.(4-5,16,19)

A relationship between 1,25(OH)₂D levels and BMD was not found. While 1,25(OH)₂D is thought to be the active form of vitamin D, many tissues express 1-α hydroxylase, and may be able to convert circulating 25(OH)D to its active form locally. (46) Circulating 25(OH)D levels are generally considered to better reflect overall vitamin D stores. (2) The results describe herein are in agreement with this, suggesting that total circulating total or free 1,25(OH)₂D levels are not good measures of vitamin D activity. This is analogous to the accepted model for the measurement of thyroid hormone action, where free T4 levels are a better measure of thyroid hormone action than circulating free T3 levels, even though T3 is the active form of the hormone.(47)

The use of standardized immunoassays for vitamin D, DBP, and albumin combined with standard calculation methods would allow the approach described herein to be adopted with more confidence by other clinical laboratories.

A wide distribution of DBP levels among our subjects and observed that DBP was negatively associated with both high BMI and black race, both of which have been associated with low 25(OH)D levels. Without wishing to be limiting, one potential explanation is that 25(OH)D might itself regulate the production of DBP. Lowering DBP levels would allow a higher fraction of DBP to be bioavailable in situations where total levels are low. Other possible explanations for the observed associations between race, BMI, and DBP levels include genetic factors and uptake of circulating DBP by adipose tissue.

Described herein is evidence that DBP modifies the relationship between 25(OH)D and BMD in humans. Our data suggest that bioavailable 25(OH)D levels are a better of measure of vitamin D activity than total 25(OH)D levels, at minimum, with respect to bone metabolism. It is therefore possible that by using total 25(OH)D levels as a measure of vitamin D sufficiency, individuals may be misclassified as vitamin D sufficient or insufficient. This may explain conflicting results of prior studies of the relationship between serum 25(OH)D concentrations and BMD. Determining which individuals have a true deficit in vitamin D may allow future vitamin D supplementation interventions to be targeted to those individuals most likely to benefit. Additionally, use of bioavailable 25(OH)D levels may further elucidate the nature of the relationship between vitamin D and a wide range of outcomes including fracture,(7) infection,(49) cancer.(50) and cardiovascular disease.(51)

Appendix. Derivation of Calculated Free and Bioavailable 25-Hydroxyvitamin D Definitions

D=25-hydroxyvitamin D (calcidiol), sum of both D2 and D3

Alb=albumin

DBP=Vitamin D binding protein, also known as Group-specific component or Gc; also referred to herein as VDBP

[D_(Alb)]=concentration of albumin-bound vitamin D

[D_(DBP)]=concentration of DBP-bound vitamin D

[D]=concentration of free (unbound) D

[Total]=concentration of Total 25OH-D=[D_(DBP)]+[D_(Alb)]+[D]

[Bio]=concentration of Bioavailable D (Bioavailable=sum of free and albumin-bound vitamin)=[D]+[D_(Alb)]

K_(alb)=affinity constant between vitamin D and albumin=6×10⁵ M⁻¹

K_(DBP)=affinity constant between vitamin D and DBP=0.7×10⁹ M⁻¹

Vitamin D Index=ratio of measured concentrations of total 25-hydroxyvitamin D and VDBP

Equations

Total 25(OH)-Vitamin D [Total]=sum of concentrations of 25(OH)-Vitamin D3 and 25(OH)-Vitamin D2 Given that [Total]=[D]+[D _(Alb) ]+[D _(DBP)] thus [D _(DBP)]=[Total]−[D _(Alb) ]−[D]  (Eq. 1)

Albumin [Alb]=serum albumin concentration in g/L÷66,430 g/mole [D]+[Alb]

[D _(Alb)] Albumin association constant K _(alb) =[D _(Alb)]÷([D]·[Alb]) Thus [D _(Alb) ]=K _(alb)·[Alb]·[D]  (Eq. 2)

-   -   (NB: [Alb] in this example denotes the concentration of free         non-vitamin bound albumin. However, given the low affinity         between albumin and Vit. D, the concentrations of total albumin         and unbound albumin are effectively equivalent ([Total         Albumin]≈[Alb]). As a result, [Alb] may be estimated accurately         by measurements of total serum albumin.)

DBP [Total DBP]=concentration of serum DBP in g/L÷58,000 g/mole [DBP]=free unbound DBP and [D _(DBP)]=vitamin-bound DBP Given that [D]+[DBP]

[D _(DBP)] And DBP association constant K _(DBP) =[D _(DBP)]÷([DBP]·[D]) Thus [D]=[D _(DBP) ]÷K _(DBP)÷[DBP]  (Eq. 3) Since [Total DBP]=sum of bound and unbound DBP=[DBP]+[D _(DBP)] Therefore [DBP]=[Total DBP]−[D _(DBP)]  (Eq. 4)

Solving for Free 25(OH)-Vitamin D

From Eqs. 3 and 4 we see that: [D]=[D _(DBP) ]÷K _(DBP)÷([Total DBP]−[D _(DBP)])  (Eq. 5) If we substitute Eq. 1 into Eq. 2, we find that: [D _(DBP)]=[Total]−(K _(alb)·[Alb]+1)·[D]  (Eq. 6)

Substituting Eq. 6 into Eq. 5 produces the following: [D]={[Total]−(K _(alb)·[Alb]+1)·[D]}÷K _(DBP)÷([Total DBP]−{[Total]−(K _(alb)·[Alb]+1)·[D]})

The equation is now limited to known constants (K_(DBP) and K_(alb)), measured values ([Total DBP], [Alb], and [Total]) and the dependent variable for free vitamin D [D]. After propagating products and several rearrangements we can further simplify this to fit the form of a second-degree polynomial: ax ² +bx+c=0

Where x=[D]=the concentration of free 25(OH)-Vitamin D a=K _(DBP) ·K _(alb)·[Alb]+K _(DBP) b=K _(DBP)·[Total DBP]−K _(DBP)·[Total]+K _(alb)·[Alb]+1 c=−[Total]

This polynomial may be solved for [D] using the quadratic equation: [D]=[−b+√b2−4ac]÷2a

-   -   After solving for free 25(011)-vitamin D, we may then use Eq. 2         to calculate the concentration of bioavailable (non-DBP bound         vitamin):         [Bio]=[D]+[D _(Alb)]=(K _(alb)·[Alb]+1)·[D]  (Eq. 7)         Vitamin D Index=[Total]/[Total DBP]   (Eq. 8)

Example Calculation Total 25(OH)-vitamin D=[Total]=40 ng/mL=1.0×10⁻⁷ mol/L Total serum DBP=[Total DBP]=250 ug/mL=4.3×10⁻⁶ mol/L Total serum albumin=[Alb]=4.3 g/dL=6.4×10⁻⁴ mol/L K _(alb)=6×10⁵M⁻¹ K _(DBP)=7.0×10⁸M⁻¹ a=2.7×10¹¹ b=3325 c=−1×10⁻⁷ Calculated concentration of free 25(OH)D=3.01×10⁻¹¹ mol/L=12.1 pg/mL Calculated concentration of bioavailable 25(OH)D=1.09×10⁻⁸ mol/L=4.6 ng/mL

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J Clin Endocrinol     Metab 66(6):1247-50. -   36. Halioua L, Anderson J J 1989 Lifetime calcium intake and     physical activity habits: independent and combined effects on the     radial bone of healthy premenopausal Caucasian women. Am J Clin Nutr     49(3):534-41. -   37. Schneider G B, Benis K A, Flay N W, Ireland R A, Popoff S N 1995     Effects of vitamin D binding protein-macrophage activating factor     (DBP-MAF) infusion on bone resorption in two osteopetrotic     mutations. Bone 16(6):657-62. -   38. Fang Y, van Meurs J B, Arp P, van Leeuwen J P, Hofman A, Pols H     A, Uitterlinden A G 2009 Vitamin D binding protein genotype and     osteoporosis. Calcif Tissue Int 85(2):85-93. -   39. Sinotte M, Diorio C, Berube S, Pollak M, Brisson J 2009 Genetic     polymorphisms of the vitamin D binding protein and plasma     concentrations of 25-hydroxyvitamin D in premenopausal women. Am J     Clin Nutr 89(2):634-40. -   40. Engelman C D, Fingerlin T E, Langefeld C D, Hicks P J, Rich S S,     Wagenknecht L E, Bowden D W, Norris J M 2008 Genetic and     environmental determinants of 25-hydroxyvitamin D and     1,25-dihydroxyvitamin D levels in Hispanic and African Americans. J     Clin Endocrinol Metab 93(9):3381-8. -   41. Al-oanzi Z H, Tuck S P, Raj N, Harrop J S, Summers G D, Cook D     B, Francis R M, Datta H K 2006 Assessment of vitamin D status in     male osteoporosis. Clin Chem 52(2):248-54. -   42. Lauridsen A L, Vestergaard P, Hermann A P, Brot C, Heickendorff     L, Mosekilde L, Nexo E 2005 Plasma concentrations of     25-hydroxy-vitamin D and 1,25-dihydroxy-vitamin D are related to the     phenotype of Gc (vitamin D-binding protein): a cross-sectional study     on 595 early postmenopausal women. Calcif Tissue Int 77(1):15-22. -   43. Al-oanzi Z H, Tuck S P, Mastana S S, Summers G D, Cook D B,     Francis R M, Datta HK 2008 Vitamin D-binding protein gene     microsatellite polymorphism influences BMD and risk of fractures in     men. Osteoporos Int 19(7):951-60. -   44. Snijder M B, van Dam R M, Visser M, Deeg D J, Dekker J M, Bouter     L M, Seidell J C, Lips P 2005 Adiposity in relation to vitamin D     status and parathyroid hormone levels: a population-based study in     older men and women. J Clin Endocrinol Metab 90(7):4119-23. -   45. Cauley J A, Lui L Y, Ensrud K E, Zmuda J M, Stone K L, Hochberg     M C, Cummings S R 2005 Bone mineral density and the risk of incident     nonspinal fractures in black and white women. JAMA 293(17):2102-8. -   46. van Driel M, Koedam M, Buurman C J, Hewison M, Chiba H,     Uitterlinden A G, Pols H A, van Leeuwen J P 2006 Evidence for     auto/paracrine actions of vitamin D in bone: 1alphahydroxylase     expression and activity in human bone cells. FASEB J 20(13):2417-9. -   47. Brent G A 1994 The molecular basis of thyroid hormone action. N     Engl J Med 331(13):847-53. -   48. van Hoof H J, Swinkels L M, Ross H A, Sweep C G, Benraad T J     1998 Determination of non-protein-bound plasma 1,25-dihydroxyvitamin     D by symmetric (rate) dialysis. Anal Biochem 258(2):176-83. -   49. Ginde A A, Mansbach J M, Camargo C A, Jr. 2009 Association     between serum 25-hydroxyvitamin D level and upper respiratory tract     infection in the Third National Health and Nutrition Examination     Survey. Arch Intern Med 169(4):384-90. -   50. Wactawski-Wende J, Kotchen J M, Anderson G L, Assaf A R, Brunner     R L, O'Sullivan M J, Margolis K L, Ockene J K, Phillips L, Pottern     L, Prentice R L, Robbins J, Rohan T E, Sarto G E, Sharma S,     Stefanick M L, Van Horn L, Wallace R B, Whitlock E, Bassford T,     Beresford S A, Black H R, Bonds D E, Brzyski R G, Caan B, Chlebowski     R T, Cochrane B, Garland C, Gass M. Hays J, Heiss G. Hendrix S L,     Howard B V, Hsia J. Hubbell F A, Jackson R D, Johnson K C, Judd H,     Kooperberg C L, Kuller L H, LaCroix A Z, Lane D S, Langer R D,     Lasser N L, Lewis C E, Limacher M C, Manson J E 2006 Calcium plus     vitamin D supplementation and the risk of colorectal cancer. N Engl     J Med 354(7):684-96. -   51. Wang T J, Pencina M J, Booth S L, Jacques P F, Ingelsson E,     Lanier K, Benjamin E J, D'Agostino R B, Wolf M, Vasan R S 2008     Vitamin D deficiency and risk of cardiovascular disease. Circulation     117(4):503-11.

Example 2: Bioavailable Vitamin D and Mineral Metabolism

Prior studies have yielded conflicting results regarding the association between 25-hydroxyvitamin D (25(OH)D) levels and mineral metabolism in end-stage renal disease (ESRD). Described herein are experiments testing the hypothesis that bioavailable vitamin D, the vitamin D fraction not bound to vitamin D binding protein (DBP), would associate more strongly with measures of mineral metabolism than total levels. Eighty nine patients with previously measured 25(OH)D and 1,25-dihydroxyvitamin D (1,25(OH)₂D) levels were identified from a cohort of incident U.S. dialysis patients. Stored serum samples were used to measure DBP, determine bioavailable 25(OH)D and 1,25(OH)₂D using previously validated formulae, and examine associations with measures of mineral metabolism and demographic factors. Both bioavailable 25(OH)D and bioavailable 1,25(OH)₂D were correlated with serum calcium (r=0.26, p=0.01 and r=0.23, p=0.02, respectively) whereas this association was absent for both total 25(OH)D (r=0.01, p=0.92) and total 1,25(OH)₂D (r=0.08, p=0.44). Racial differences in DBP and total 25(OH)D, but not bioavailable vitamin D, were observed. In univariate and multivariate regression analysis, only bioavailable 25(OH)D was associated with parathyroid hormone levels (p=0.007 and p=0.02, respectively). Accordingly, bioavailable 25(OH)D levels are better correlated with measures of mineral metabolism than total 25(OH)D levels in patients on hemodialysis.

Chronic kidney disease-associated mineral and bone disorder (CKD-MBD) is one of the most appreciated metabolic complications of CKD. As individuals progress toward end-stage renal disease (ESRD), declining renal 1a-hydroxylase activity leads to decreased conversion of 25-hydroxyvitamin D (25(OH)D) to the active 1,25-dihydroxyvitamin D (1,25(OH)₂D). These metabolic changes are believed to precipitate the hypocalcemia and secondary hyperparathyroidism that characterize CKD-MBD. Although 1,25(OH)₂D is thought to be the biologically active moiety, the majority of vitamin D circulates as 25(OH)D.(1) Low levels of 25(OH)D are common in ESRD; 79% of patients initiating dialysis have 25(OH)D levels below 30 ng/ml, and serum levels below this threshold are nearly universal among black ESRD patients.(2)

The free hormone hypothesis suggests that protein-bound hormones are relatively inactive while those liberated from binding proteins are free to exert biological activity.(3) For some hormones (e.g. testosterone), binding to albumin is considerably weaker than to a specific binding protein. Thus, albumin-bound hormone is often grouped with the free fraction and referred to as the “bioavailable” fraction. The majority (85-90%) of circulating 25(OH)D and 1,25(OH)D is tightly bound to vitamin D binding protein (DBP), with a smaller amount (10-15%) loosely bound to albumin. Less than 1% of circulating vitamin D exists in a free, unbound form.(4,5) Described herein are experiments testing the hypothesis that the relationship between vitamin D and markers of mineral metabolism (e.g. PTH and calcium) in ESRD would be strengthened by use of DBP and albumin to determine bioavailable vitamin D levels. Given the patterns observed in other cohorts, it was further hypothesized that the lower 25(OH)D levels typically seen in black dialysis patients would be associated with lower and not necessarily lower bioavailable vitamin D levels in this group.(6,7)

Results

Baseline characteristics of the 94 subjects included in this analysis, which are similar to those of a typical US hemodialysis population, are summarized in Table 5. None of the included subjects were recorded as receiving treatment with activated vitamin D, ergocalciferol, or cholecalciferol before initiating dialysis.

Mineral Metabolism and Vitamin D.

Baseline corrected calcium levels, measured within 14 days of chronic hemodialysis initiation, were not associated with total levels of either 25(OH)D (r=0.01, P=0.92) or 1,25(OH)₂D (r=0.08, P=0.44). In contrast, calcium levels correlated positively with both bioavailable 25(OH)D (r=0.26, p=0.01) and bioavailable 1,25(OH)₂D (r=0.23, p=0.02). These relationships are plotted in FIG. 2. A single individual with the highest bioavailable 25(OH)D and bioavailable 1,25(OH)₂D appeared to be an outlier with respect to the observed relationships, with both levels over 4 standard deviations above the mean. To examine the impact of this single data point, a sensitivity analysis was performed by repeating the analysis with this individual excluded. The relationship of calcium with bioavailable 25(OH)D (r=0.30, p=0.003) and bioavailable 1,25(OH)₂D (r=0.27, p=0.008) were both somewhat strengthened.

Phosphorus levels demonstrated no association with either total levels of 25(OH)D (r=0.14, P=0.19) or 1,25(OH)₂D (r=0.01, P=0.94). Similarly, neither bioavailable 25(OH)D (r=−0.10. P=0.32) nor bioavailable 1,25(OH)₂D (r=−0.16, P=0.12) were significantly associated with phosphorus levels.

Alkaline phosphatase was not associated with either total or bioavailable forms of 25(OH)D or 1,25(OH)₂D (p>0.05 for all comparisons).

The relationship between PTH and all four forms of vitamin D were examined in univariate and multivariate regression models. In univariate models, only bioavailable 25(OH)D was associated with PTH, with a −0.35 log decrease in PTH for each log increase in bioavailable 25(OH)D (p=0.01). In a multivariate model controlling for age, gender, race, and survival status at one year, this relationship remained unchanged (β=−0.32, p=0.02). A third model adding calcium, phosphorus, and bioavailable 1,25(OH)2D levels demonstrated similar results (Table 7). As with the calcium findings, both the unadjusted and adjusted coefficients became stronger when a single outlier was excluded (unadjusted: β=−0.40, p=0.003; adjusted: β=−0.36, p=0.01). In contrast, there was no significant association between total 25(OH)D and PTH (FIG. 3).

Patient Factors and Vitamin D.

Older individuals had higher total 25(OH)D levels (r=0.31, P=0.003) and bioavailable 25(OH)D (r=0.21, p=0.04). Neither total nor bioavailable 1,25(OH)₂D were associated with age. Female gender was associated with lower total 25(OH)D levels (median in men: 22.0 ng/dl, in women: 18.0 ng/dl; p=0.03). While females had numerically lower median total 1,25(OH)₂D and bioavailable 25(OH)D and 1,25(OH)₂D levels, none of these differences were statistically significant.

Black individuals had lower total 25(OH)D levels (median: 15.2 vs 23.2 ng/ml, p<0.001) but not bioavailable 25(OH)D levels (median: 3.8 vs. 2.8 ng/ml, p=0.21). The contrast in racial differences between these two forms of vitamin D was driven largely by lower DBP levels among blacks. This difference persisted even when examining only individuals who survived for one year on dialysis or those who died in this timeframe (Table 6). PTH levels did not differ significantly by race (median: 201 pg/ml [black] vs. 168 pg/ml [white], p=0.47). Neither total nor bioavailable 1,25(OH)₂D levels differed by race (p=0.07 and 0.49, respectively). Of note, we found no racial differences in systolic or diastolic blood pressure, diabetes, or BMI.

The study was not specifically powered to address whether systolic and diastolic blood pressure, BMI, and survival or a diagnosis of diabetic nephropathy or diabetes were associated with any form of vitamin D (data not shown).

Sensitivity Analysis.

Sensitivity analyses were performed to address the possibility that uremia might alter DBP's binding affinity with 25(OH)D or 1,25(OH)₂D. With DBP-binding coefficients that were 25% lower than those originally determined by Bikle, et al., (4,5) bioavailable measures of both 25(OH)D (r=0.26, p=0.01) and 1,25(OH)₂D (r=0.22, p=0.03) remained associated with corrected calcium. Similar results were observed with 25% higher coefficients (bioavailable 25(OH)D:r=0.27, p=0.009; bioavailable 1,25(OH)₂D (r=0.24, p=0.02). Associations of bioavailable 25(OH)D with PTH remained statistically significant in both cases, with association coefficients changing less than 12% in either univariate or multivariate analyses.

Discussion

Using a retrospective cohort of incident dialysis patients, the relationship between measures of mineral metabolism (including serum calcium and PTH) and both total and bioavailable levels of vitamin D was examined. Described herein are results indicating that bioavailable 25(OH)D is associated with both corrected serum calcium levels and PTH, both of which are well-established measures of mineral metabolism in ESRD, while total 25(OH)D demonstrates no such associations. This data builds upon prior findings described elsewhere herein: analysis from two separate cohorts now support the hypothesis that bioavailable measures of vitamin D, which take into account binding of vitamin D to albumin and DBP, are more relevant to biological outcomes than are total levels, which are currently the standard measure of vitamin D status.

Some in vitro studies suggest that DBP-binding limits vitamin D activity in multiple target cells.(8,9) Studies of DBP-null mice have shown that these animals display markedly reduced levels of 25(OH)D and 1,25(OH)₂D compared with wild-type mice, with a markedly reduced half-life.(10) Despite their low vitamin concentrations, when these mice are provided with a steady source of dietary vitamin D, they show no differences in serum calcium, phosphorus, alkaline phosphatase, and PTH compared to wild-type controls. These studies support the application of the free hormone hypothesis to vitamin D physiology, at least for some biological actions. Despite these findings, uptake of protein-bound hormone in cells expressing megalin appears to be important for some processes, so the biology underlying the findings described herein may be more complex than is immediately apparent and warrants further investigation.(11,12)

Black patients were oversampled as the data presented in Example 1 suggested blacks have lower DBP levels than whites, an observation supported by the data described in this Example. As previously reported, the inventors and others observed that black race is associated with lower levels of total 25(OH)D.(2,13) As might be expected from these two parallel racial differences (lower total 25(OH)D and lower DBP in blacks vs. whites), the levels of bioavailable 25(OH)D are similar, as described herein.

Despite similar bioavailable D levels between racial groups, and association between bioavailable 25(OH)D and PTH, black patients had numerically higher PTH levels than their white counterparts. Though this difference was not statistically significant in the sample used herein, larger samples from this cohort have found significantly higher levels of PTH in black individuals.(14) Bioavailable 25(OH)D did not differ by race, yet were negatively associated with PTH, suggesting that racial differences in PTH are not primarily driven by differences in 25(OH)D. Indeed, others have found that PTH levels in blacks are higher than those in whites, even in states of 25(OH)D sufficiency.(13)

Several studies have attempted to assess the metabolic consequences of low 25(OH)D levels in advanced CKD and ESRD, but have yielded conflicting results. Ergocalciferol, a form of nutritional vitamin D that can increase 25(OH)D levels, appears to affect parathyroid hormone (PTH) levels in stage 3, but not in stage 4, CKD.(15,16) Moreover, some studies have demonstrated a significant association between 25(OH)D levels and PTH in ESRD,(17-19) while others have not.(20,21) Associations between 25(OH)D and serum calcium have been similarly mixed.(2,17,22)

This contradictory data has led to confusion about the role that repeating 25(OH)D (e.g. with nutritional forms of vitamin D such as cholecalciferol or ergocalciferol) plays in the management of patients with ERSD.(23,24) In order to study the role of vitamin D insufficiency and identify patients who are most likely to benefit from repletion, it is critical to have a biologically relevant measure of vitamin D status. Notably, the experiments described herein failed to find any significant link between total or bioavailable 1,25(OH)₂D and relevant measures of mineral metabolism, echoing the general consensus that circulating serum levels of the active hormone are not useful as a measure of vitamin D status.(1)

A relationship between survival and vitamin D status was not found, though this sample had considerably less power to detect this relationship than prior studies, which have found that severe vitamin D insufficiency (typically defined levels <10 ng/ml) is associated with increased mortality.(19, 25, 26)

None of the individuals in this analysis, who initiated dialysis in 2004 or 2005, had been treated with activated vitamin D analogs prior to initiating dialysis.

PTH is commonly used as a proxy for metabolic bone disease in dialysis patients, but has an imperfect association with bone disease.(27) Bone biopsies and non-invasive measures of bone density and structure were not available in this study and are potential targets for future analyses. As described in Example 1 herein, a relationship between bioavailable 25(OH)D and bone density in a healthy population,(6) has been demonstrated but it is not certain that this relationship will extend to the ESRD population given known alterations in mineral metabolism. Metabolic changes that accompany ESRD and/or dialysis, as well as genetic variants in DBP or other relevant proteins, have the potential to influence binding of 25(OH)D to DBP. Whereas the sensitivity analysis did not indicate that these factors are likely to affect the fundamental findings of this study, studies that directly measure bound and unbound fractions could improve upon the initial estimates and the equations used herein. Lastly, it is possible that measured 25(OH)D levels in this study were influenced by levels of 24,25(O)₂D. Confirmation of the findings described herein with assays able to differentiate 25(OH)D, 24,25(OH)₂D, and 1,24,25(OH)₃D may further elucidate these biological relationships.

This study provides additional evidence to support the notion that bioavailable, rather than total, levels of vitamin D may be more relevant measures of vitamin D status with respect to its actions on mineral metabolism. While mineral metabolism has been the traditional focus of vitamin D actions, recent data suggest that its actions may be more widespread, with effects on the immune response,(28) hypertension.(29) and insulin sensitivity.(30), among others.

Methods

Accelerated Mortality on Renal Replacement (ArMORR) is a nationally representative prospective cohort study of incident chronic hemodialysis patients (n=10,044) who began renal replacement between Jul. 1, 2004 and Jul. 30, 2005 at one of 1,056 dialysis centers in the U.S. operated by Fresenius Medical Care, North America (FMC).(31) The ArMORR dataset contains a broad range of demographic and clinical data including co-existing medical conditions, laboratory results, as well as serum and plasma samples. Clinical data were collected prospectively, entered uniformly into a central database by practitioners at the point of care. All clinical data arriving at Fresenius undergo rigorous data quality assurance and quality control (QA/QC) auditing. Blood samples collected for clinical care were shipped to and processed by a central laboratory (Spectra East, Rockland, N.J. USA). After processing for routine clinical testing, remnant samples were shipped on ice to the ArMORR Investigators where the samples were aliquoted and stored in liquid nitrogen. This study was approved by the Institutional Review Board of the Massachusetts General Hospital, which waived the requirement for informed consent, and conducted in accordance with its ethical standards and the Declaration of Helsinki.

Study Population.

Between Jul. 1, 2004 and Jun. 30, 2005, 10,044 incident hemodialysis patients were prospectively enrolled into ArMORR. Subjects were identified who had 25(OH)D and 1,25(OH)₂D levels previously measured as part of a case-control survival study.(19) Based on prior results in a healthy population, we set a minimum sample size of 80 subjects. To ensure adequate power for racial comparisons, an approximately equal number of black (n=24) and white (n=23) patients were randomly selected from the controls, and an equal number of race-matched cases. Thus, the total sample size was n=94. Baseline laboratory values were measured from samples collected within 14 days of dialysis initiation.

Assays.

Total 25(OH)D and 1,25(OH)₂D were previously measured from thawed samples in duplicate using a commercially available radioimmunoassay (DiaSorin Inc, Stillwater, Minn., USA). The interassay coefficients of variation (CVs) for 25(OH)D were <3% at levels <30 ng/ml and for 1,25(OH)₂D were <6.5% at levels <32.5 pg/ml. Intact PTH (1-84) was measured using the Nichols Advantage Biointact-PTH assay by the centralized laboratory.

DBP was measured in duplicate in thawed serum samples by commercial enzyme linked immunosorbent assay (ELISA) (R&D Systems, Minneapolis, Minn., Catalog Number DVDBP0) according to the manufacturer's instructions. The assay was conducted after diluting serum samples 1 to 2,(00)0 in Calibrator Diluent RD6-11 (R&D Systems Part Number 895489). Inter-assay CV was 8.5% at a concentration of 40 μg/ml. The assay recovered between 93 and 110% of a 100-200 μg/mL dose of exogenous DBP added to human serum samples containing between 25-200 μg/mL of endogenous DBP. There were no differences in the recovery of exogenous DBP in black patients or obese patients. The manufacturer reports no significant cross-reactivity with human albumin or vitamin D3. DBP levels were below the detection limit in 5 black patients who died within the first year of dialysis. These individuals were assigned a DBP value equal to the lowest detectable level (12.3 μg/dl).

Calculation of Bioavailable Vitamin D.

Equilibrium dialysis and centrifugal ultrafiltration dialysis have previously been used by some investigators to indirectly measure free vitamin D levels, allowing estimation of the binding affinity constants for 25(OH)D and 1,25(OH)₂D with DBP and albumin.(4,5,32) In these studies, calculated levels of free 25(OH)D and levels measured by centrifugal ultrafiltration were highly correlated (r=0.925).(5) Bioavailable and free vitamin D were calculated as described in Example 1 herein.

Bioavailable 1,25(011)₂D levels were determined using the same approach using affinity constants previously derived by centrifugal ultrafiltration dialysis.(4) These affinity constants were previously validated in both healthy and cirrhotic individuals,(4,5) but have not been directly assessed in hemodialysis patients. Therefore a sensitivity analysis of the main findings was performed using DBP binding coefficients for 25(OH)D and 1,25(OH)₂D that were 25% higher or 25% lower than previously measured values.

Statistical Analysis.

Prior to analysis, given the role of albumin as a binding protein for both vitamin D and calcium, serum calcium levels were corrected for albumin using the following equation: corrected calcium=total calcium+0.8*(4-albumin).(34) Spearman correlation analysis was performed to assess linear associations. Group comparisons of vitamin D levels were performed using the Wilcoxon rank sum test. To examine multivariable associations between bioavailable vitamin D and PTH, both variables (because of non-normal distribution) were natural-log transformed and analyzed using multivariate linear regression. All analyses were conducted using STATA Statistical Software (College Station, Tex.) version 11.

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Impact of     Ergocalciferol Treatment of Vitamin D Deficiency on Serum     Parathyroid Hormone Concentrations in Chronic Kidney Disease. Am J     Nephrol. 2007; 27(1):36-43. -   16. Al-Aly Z, Qazi R A, González E A, Zeringue A, Martin K J.     Changes in serum 25-hydroxyvitamin D and plasma intact PTH levels     following treatment with ergocalciferol in patients with CKD. Am J     Kidney Dis. 2007 Jul. 1; 50(1):59-68. -   17. Jean G, Charra B, Chazot C. Vitamin D Deficiency and Associated     Factors in Hemodialysis Patients. J Ren Nutr. 2008 September;     18(5):395-399. -   18. Ravani P, Malberti F. Tripepi G, Pecchini P, Cutrupi S.     Pizini P. et al. Vitamin D levels and patient outcome in chronic     kidney disease. Kidney Int. 2009 Jan. 1; 75(1):88-95. -   19. Wolf M, Shah A, Gutierrez O, Ankers E, Monroy M, Tamez H, et al.     Vitamin D levels and early mortality among incident hemodialysis     patients. Kidney Int. 2007 Oct. 1; 72(8):1004-1013. -   20. González E A, Sachdeva A, Oliver D A, Martin K J. Vitamin D     insufficiency and deficiency in chronic kidney disease. A single     center observational study. Am J Nephrol. 2004 August;     24(5):503-510. -   21. London G M, Guèrin A P, Verbeke F H, Pannier B, Boutouyrie P,     Marchais S J, et al. Mineral metabolism and arterial functions in     end-stage renal disease; potential role of 25-hydroxyvitamin D     deficiency. J Am Soc Nephrol. 2007 Feb. 1; 8(2):613-620. -   22. London G M, Marty C, Marchais S J, Guerin A P, Metivier F, de     Vernejoul M-C. Arterial calcifications and bone histomorphometry in     end-stage renal disease. J Am Soc Nephrol. 2004 Jul. 1;     15(7):1943-1951. -   23. Nigwekar S U, Bhan I, Thadhani R. Nutritional vitamin D in     dialysis patients: what to D-iscern?Nephrology Dialysis     Transplantation. 2011 March; 26(3):764-766. -   24. Bhan I, Hewison M, Thadhani R. Dietary vitamin D intake in     advanced CKD/ESRD. Semin Dial. 2010 June; 23(4):407-410. -   25. Drechsler C. Pilz S, Obermayer-Pietsch B, Verduijn M, Tomaschitz     A, Krane V, et al. Vitamin D deficiency is associated with sudden     cardiac death, combined cardiovascular events, and mortality in     haemodialysis patients. Eur Heart J. 2010 September;     31(18):2253-2261. -   26. Drechsler C, Verduijn M, Pilz S, Dekker F W, Krediet R T, Ritz     E, et al. Vitamin D status and clinical outcomes in incident     dialysis patients: results from the NECOSAD study. Nephrol Dial     Transplant. 2011 March; 26(3): 1024-1032. -   27. Ott S M. Review article: Bone density in patients with chronic     kidney disease stages 4-5. Nephrology. 2009 June; 14(4):395-403. -   28. Bhan I, Camargo C A, Wenger J, Ricciardi C, Ye J, Borregaard N,     et al. Circulating levels of 25-hydroxyvitamin D and human     cathelicidin in healthy adults. J Allergy Clin Immunol. 2011 May;     127(5):1302-4.e1. -   29. Forman J P, Giovannucci E, Holmes M D, Bischoff-Ferrari H A,     Tworoger S S, Willett W C, et al. Plasma 25-hydroxyvitamin D levels     and risk of incident hypertension. Hypertension. 2007 May;     49(5):1063-1069. -   30. Chonchol M, Scragg R. 25-Hydroxyvitamin D, insulin resistance,     and kidney function in the Third National Health and Nutrition     Examination Survey. Kidney Int. 2007 Jan. 1; 71(2):134-139. -   31. Gombart A F, Bhan I, Borregaard N, Tamez H, Camargo C A,     Koeffler H P. et al. Low plasma level of cathelicidin antimicrobial     peptide (hCAP18) predicts increased infectious disease mortality in     patients undergoing hemodialysis. Clin. Infect. Dis. 2009 Feb. 15;     48(4):418-424. -   32. van Hoof H J, Swinkels L M, Ross H A, Sweep C G, Benraad T J.     Determination of non-protein-bound plasma 1,25-dihydroxyvitamin D by     symmetric (rate) dialysis. Anal. Biochem. 1998 May 1;     258(2):176-183. -   33. Vermeulen A, Verdonck L, Kaufman J M. A critical evaluation of     simple methods for the estimation of free testosterone in serum. J     Clin Endocrinol Metab. 1999 October; 84(10):3666-3672. -   34. Correcting the calcium. Br Med J. 1977 Mar. 5; 1(6061):598.

Example 3: Bioavailable Vitamin D in Pregnant Women

A pilot study in pregnant women enrolled in the MOMS cohort was conducted to determine if VDBP modifies the relationship between first trimester 25(OH)D levels and subsequent development of preeclampsia or gestational diabetes. Although the sample sizes in pregnant women were small, total 25(OH)D levels were significantly lower among blacks (18.8 [10.8-24.2] ng/mL, n=9), Hispanics (21.4 [16.7-27.7] ng/mL n=61), and Asians (22.5 [14.8-29.7] ng/ml, n=8) compared to white non-Hispanics (32.1 [26.3-36.6] ng/mL, n=127; P<0.03 for all comparisons). VDBP levels were significantly lower in blacks (97.2 [73.6-361.2] μg/ml) compared to whites (504 [338-700]μg/ml, P<0.001). Bioavailable 25(OH)D levels were similar in white and black subjects.

Example 4: Bioavailable Vitamin D and Racial Variability

Black individuals consistently have low 25-hydroxy vitamin D (25[OH)D]levels¹⁵⁻¹⁹ and are at especially high risk for poor outcomes linked to vitamin D sufficiency.¹⁵ Paradoxically, blacks have higher BMD and a lower risk of osteoporosis than whites.²⁰ Although 25(OH)D is the marker currently considered most suitable for assessing vitamin D status,^(2,21) studies have shown a weaker relationship of 25(OH)D to BMD in blacks and other minorities compared to whites.^(18,19,22,23) Importantly, the BMD-vitamin D relationship in blacks needs clarification.¹⁸⁻²⁰ and questions about how to define clinically relevant vitamin D insufficiency, the impact of race on measures of vitamin D status, how to reliably identify who needs supplementation with vitamin D (and with how much) to favorably impact disease outcomes remain unanswered.^(2,15)

The research described herein has the potential to redefine who is vitamin D deficient and to significantly improve diagnosis and the efficiency of strategies for prophylaxis and treatment. The hypothesis that invokes the free hormone hypothesis in regards to bioavailable vitamin D can be investigated using a large cohort of black and white subjects enrolled in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study. Studies described in Examples 1, 2 and 3 herein in various populations (healthy volunteers, individuals with end-stage renal disease (ESRD), pregnant women) measured VDBP, total 25(OH)D and calculated free 25(OH)D. These results indicate that 25(OH)D levels are directly correlated with VDBP levels and inversely correlated with free 25(OH)D levels. The data also reveal substantial racial differences in VDBP levels. Blacks had 25-60% lower VDBP levels than whites, while free and bioavailable 25(OH)D levels were similar. In healthy adults, non-VDBP bound 25(OH)D levels were strongly associated with BMD, whereas total 25(OH)D levels and PTH were not.²³ After adjusting for race in patients with ESRD, both VDBP and free 25(OH)D (but not total 25(OH)D), were associated with PTH.³¹ These correlations (or lack thereof) between unbound vs total 25(OH)D and BMD and racial differences in VDBP levels led to the hypothesis that VDBP modifies the relationship between BMD and 25(OH)D.²³ Total 25(OH)D may not faithfully reflect physiologically relevant vitamin D status, particularly in relation to BMD and questions the clinical relevance of 25(OH)D assays in all races.³³

VDBP levels may be the previously unrecognized link that explains the BMD-vitamin D paradox in blacks. Using stored blood samples from black and white subjects enrolled in HANDLS (n˜2,200), the following hypotheses can be tested: 1. Blacks have lower levels of VDBP and total 25(OH)D levels, but similar levels of free and bioavailable 25(OH)D as whites. 2. Free and bioavailable 25(OH)D levels are independently associated with BMD in blacks and whites, inversely and linearly associated with PTH levels, and these associations are stronger than those between total 25(OH)D and BMD.

Aim 1: To determine VDBP, total and bioavailable 25(OH)D, and PTH levels in blacks vs whites.

Aim 2: To test for associations between BMD, bioavailable 25(OH)D, and PTH compared to total 25(OH)D in blacks vs whites.

The studies described herein, (1) apply well-established mechanisms of hormone biology; (2) demonstrate that bioavailable/free 25(OH)D is more strongly associated with outcomes than total 25(OH)D; (3) can aid future clinical trial designs in which vitamin D insufficiency will be redefined: (4) aim to individualize diagnosis and treatment based on race to improve therapeutic and cost-efficiency of our limited health care resources, and (5) question current public health paradigms for clinical decision-making about who is vitamin D deficient, who should be treated, and who can avoid being treated.

25(OH)D Insufficiency is Even More Common in Blacks than in Whites.

According to current cutoffs defining vitamin D deficiency in terms of 25(OH)D, approximately 50% of African Americans in the US are either chronically or seasonally at risk.⁴⁸ Racial disparities in vitamin D status between blacks and whites may arise from insufficient dietary intake or impaired conversion of vitamin D by sunlight due to skin pigmentation.¹⁶ Holick⁴⁸ reported that in Boston, 84% of black men and women >65 years old were vitamin D deficient at the end of the summer, which is typically when vitamin D levels are highest. Deficiency was attributed to several factors including insufficient milk intake because of lactose intolerance, decreased synthesis of vitamin D3 in the skin due to pigmentation, and avoidance of sun exposure to minimize skin pigmentation.⁴⁸ According to the 1988-1994 National Health and Nutrition Examination Survey (NHANES)III, 42% of black women (15-49 years old) were vitamin D deficient at the end of the winter compared to 4% of white women.⁴⁹ Concentrations in serum of 25(OH)D measured during different seasons showed substantially lower levels in blacks (adjusted for body weight and vitamin D intake) throughout all seasons and smaller seasonal increases during summer months than whites.⁵⁰ These racial differences are reinforced in more recent NHANES 2001-2006 data.^(22,51) Table 9 summarizes several representative studies reporting vitamin D levels in blacks vs whites. In most studies, the discrepancy between races does not extend to 1,25 (OH)₂D levels, which are generally similar in blacks and whites.^(50,52)

As described in Example 2 herein, data from ArMORR (Accelerated Mortality in Renal Replacement which includes ESRD patients at the initiation of dialysis prior to any vitamin D replacement) demonstrated that mean 25(OH)D levels were 23.2±13.7 (SD) ng/mL in whites (n=653) and 16.9±10.9 in blacks (n=372) (P<0.05). Similar results were found from a randomly-selected race-matched sample from ArMORR in which total 25(OH)D was 27.3±15.3 ng/mL in whites (n=23) and 16.4±10.1 in blacks (n=24)(P=0.004).³¹ Given that: (1) the incidence of vitamin D insufficiency is consistently higher in blacks than whites; (2) the range of total 25(OH)D cutoff levels used to define insufficiency is wide; and (3) correlation between 25(OH)D with mineral markers and BMD is lacking,^(23,40) the public health implications of continued reliance on total 25(OH)D for diagnosis and treatment are broad. The marker used to diagnose and supplement vitamin D deficient states must be appropriate for racially diverse populations. Based on the data described in Example 2, it is hypothesized that total 25(OH)D may not be uniformly applicable to all races. The definition of vitamin D insufficiency needs to be revisited.

Improving the understanding of vitamin D status among different races is expected to have broadly significant therapeutic and public health implications. Specifically, by improving knowledge about vitamin D biology, the IOM's public health position on vitamin D replacement can be refined to consider race and VDBP levels when determining vitamin D targets.

The inventors have previously reported a curvilinear relationship between PTH and total 25(OH)D that PTH in older hospitalized patients.⁴⁰ PTH was inversely correlated to total 25(OH)D levels <15 ng/mL. A similar strong inverse correlation was observed in a large (n=825) cohort of incident dialysis patients.⁴³ At higher total 25(OH)D levels (≧15 ng/mL), the correlation with PTH was not as clear.⁴⁰ As described in Example 1, in younger healthy subjects whose mean total 25(OH)D levels were 25.7±11.1 ng/mL (64.2=27.7 nmol/L), PTH was not correlated with total, bioavailable 25(OH)D, or BMD. This suggests that the association between free or bioavailable 25(OH)D levels and BMD is not mediated via PTH in individuals whose vitamin D status is relatively normal. However, due to the relatively small sample size of the healthy cohort, these correlations may not have been evident. Example 2 indicates that, after adjusting for race, free 25(OH)D (but not total 25[OH]D) correlates with PTH.

The large HANDLS dataset (n˜2,200) can be used to determine if PTH is better and more linearly correlated with free- or bioavailable 25(OH)D than with total 25(OH)D. Additionally, the question of whether racial differences exist among these variables can be explored. By following subjects with BMD measurements at baseline for changes over time in the HANDLS cohort, the measures of vitamin D which best predict changes in BMD in different racial groups can be identified.

Why do Blacks have Lower Levels of Vitamin D yet Higher BMD than Other Races?

Despite having lower levels of 25(OH)D, blacks have higher BMD^(19,20) and a lower risk of osteoporotic fractures than whites.^(20,58,59) Although factors other than vitamin D are likely to contribute, it has been hypothesized that blacks have adaptive responses that protect the skeleton even when 25(OH)D is low. 16 Skeletal resistance to parathyroid hormone (PTH) activity and bone-sparing adaptations that promote beneficial skeletal effects of active vitamin D (1,25 dihydroxyvitamin D [1,25(OH)₂D]) have been proposed to explain this paradox.¹⁶ For example, moderately low 25(OH)D can induce PTH-stimulated synthesis of 1,25(OH)₂D in the kidney.^(60,61) Using data from NHANES 2003-2006, Gutierrez and colleagues²² observed that BMD decreased (p<0.01) with serum 25(OH)D and calcium intake among whites and Mexican-Americans, but not among blacks (p=0.2).²² They proposed that relationships between 25(OH)D, BMD, and PTH differ by race. Other studies have also shown that the relationship between 25(OH)D and BMD in blacks is weaker than in whites or is nonexistent.^(18,19)

Higher PTH levels have been reported in blacks than in non-blacks.^(22,31) Lower PTH may be related to low 25(OH)D, an adaptation to minimize urinary calcium losses and increase 1,25(OH)₂D activity. However, racial differences in PTH level persist even when total 25(OH)D is high,²² and PTH suppression by 25(OH)D may occur at a lower threshold in blacks versus non-blacks.^(22,62) Thus, in addition to racial differences between BMD and total 25(OH)D levels, the relationships between PTH and free- and bioavailable 25(OH)D vs total 25(OH)D may also differ by race. It is proposed herein that the VDBP hypothesis will help explain or better understand these relationships.

Although the relationship of VDBP, 25(OH)D, and BMD has not been clearly established in humans, animal studies suggest a role for VDBP in modulating the rates of bioavailability, activation, and end-organ responsiveness of vitamin D metabolism.⁶⁶ as well as a role in the BMD-25(OH)D paradox in blacks. That is, despite having lower total 25(OH)D levels, free and bioavailable 25(OH)D levels in blacks may in fact be normal or even higher than normal, as a result of relatively low VDBP concentrations as explained by the free-hormone hypothesis. Conversely, skin with light pigment captures vitamin D from the environment more readily, and higher VDBP levels may be an adaptation for regulating bioavailable vitamin D. Genetic data are collected in HANDLS and phenotyping has been performed by the HANDLS investigators with results published in peer reviewed journals.^(67,68)

The significance of circulating VDBP levels with regard to the biological activity of vitamin D in humans is unclear.^(2,18,19,21,22,24-26,30) Several properties that influence the bioavailability of vitamin D are analogous to those of the lipid-soluble androgen hormone, testosterone (T). In the circulation, total T is 60% bound to sex hormone binding globulin (SHBG), whereas 38% is albumin-bound and 2% is available as free-T.⁷⁵ Non-SHBG-bound T and free T are the biologically active components of circulating T (bio-T).⁷⁶ The method used to calculate bio-T includes measured values of total T, albumin, SHBG and their binding constants into a mathematical model of tripartite binding. A strong correlation exists between measured bio-T and calculated bio-T.⁷⁷ Using similar methods, concentrations of free and bioavailable vitamin D may be calculated using measured affinity constants to VDBP and albumin, as described in Example 1 and elsewhere herein. Calculated free D values are highly correlated with measured values of free D, as validated by Bikle et al.^(38,70) and can be used to estimate circulating free vitamin D concentrations.

Studies on the various circulating forms of vitamin D have shown that vitamin D is 85-90% bound to VDBP, 10-15% is albumin-bound, and only 1% circulates freely.⁷⁰ Given that the majority of vitamin D is bound to VDBP, what is the role of VDBP in vitamin D physiology?Multiple animal models have demonstrated that VDBP is important as a high affinity serum reservoir for Vitamin D. VDBP-deficient animals have no high affinity serum carrier for the vitamin: as a consequence of this their serum vitamin concentrations are significantly decreased, and without a high affinity carrier they rapidly excrete vitamin D in the urine. Together these events cause mice to quickly develop a vitamin insufficiency when put on diets low in Vitamin D.⁶⁶ Although these animals are prone to rapidly develop vitamin insufficiency in the absence of dietary vitamins, when dietary vitamin D is abundant, the animals are able to maintain calcium homeostasis and do not appear to suffer from hypovitaminosis.

In contrast, animals that express VDBP but are missing the receptors required for renal resorption of VDBP from glomerular ultrafiltrate display an even more dramatic phenotype. A significant amount of VDBP (and albumin) are filtered by the glomerulus.^(72,78) The filtered VDBP and albumin are normally recovered in the proximal tubules, however, by megalin/cubulin receptor-mediated endocytosis. In the absence of megalin, vitamin D is sequestered by VDBP to the urine, producing rapid and complete vitamin insufficiency even when provided with a vitamin-enriched diet, and develop severe abnormalities in calcium homeostasis and bone disease.⁷²

The conclusions drawn from these animal models support a model where VDBP and its endocytic receptors act as serum reservoirs and provide a mechanism for the prevention of urinary losses. Based upon tissue culture and animal model studies, it is unclear whether VDBP is involved in the intracellular delivery of 25(OH)D to its target tissues. The high affinity of extracellular VDBP for 25(OH)D may prevent spontaneous dissociation and diffusion into cells. Experiments in tissue culture have shown that when vitamin D-responsive osteoblasts or monocytes are treated with vitamin D, addition of VDBP in the media actually inhibits 25(OH)D endocytosis and intracellular signaling.^(73,74) Furthermore, although VDBP-deficient mice have very low serum vitamin concentrations, if they are provided with sufficient vitamin D in their diet they do not suffer from problems with calcium homeostasis, and they accumulate normal amounts of 1,25(OH)₂D in their tissues.⁷³

Together, these biochemical, tissue culture, and animal model studies suggest that although VDBP helps to prevent insensible urinary losses, retain serum vitamin levels, and maintain stable vitamin D concentrations between meals, it is not necessary for intracellular delivery of 25(OH)D or its conversion to active 1,25(OH)₂D. If VDBP is not absolutely necessary for intracellular delivery of 25(OH)D, and since albumin-bound 25(OH)D is the second most abundant circulating form of the vitamin, an alternative pathway for vitamin D delivery to the proximal tubules of the kidney and other target tissues must be considered: endocytic delivery of albumin bound vitamin D. Albumin and VDBP are in the same protein family, and they both share megalin and cubulin as their endocytic receptors. The most important target for vitamin D delivery and its actions is the epithelium of the proximal convoluted tubule (PCT). Recent evidence has unexpectedly emerged that a large amount of albumin and VDBP are filtered through the glomerular basement membrane and then resorbed in the proximal tubule.^(79,80) In the PCT, albumin is resorbed by cubulin-mediated endocytosis,⁷⁹ and VDBP is endocytosed by megalin binding (although cubilin may also play a role).^(72,78) Megalin and cubilin are part of the same receptor complex, and thus albumin and VDBP share very similar endocytic pathways. The fact that both these proteins (and any vitamin bound to them) are delivered to the renal epithelium in such large amounts suggests that either one may be a vehicle of intracellular vitamin delivery. Once these proteins are inside, however, albumin may be the principal source of diffusible 25(OH)D given its low 25(OH)D affinity compared to VDBP. It has recently been demonstrated that the large amounts of endocytosed albumin are actually transported through the renal epithelium and back to the circulation intact by transcytosis.⁸¹ Given the structural and evolutionary similarities between albumin and VDBP, and their shared endocytic receptors, it is hypothesized that VDBP also participates in transcytosis.

The transcytosis of albumin (and possibly VDBP) through renal epithelial cells described above thus saves these cells from the burden of having to degrade this mass in the lysosomes, which, based upon the estimated amounts of albumin flux would be toxic to the cells. This recent finding is significant to vitamin D bioavailability in megalin-expressing target tissues because transcytosis would also provide for an ideal autocrine mechanism for efficient intracellular delivery of vitamin D that can be regulated. As albumin transits through the cells, it would release 25(OH)D through spontaneous dissociation, providing a nearby source of vitamin D to intracellular VDBPs, CYP27B1 hydroxylase, and VDR receptors. In contrast, although VDBP should not release of much of its bound vitamin during transit through the tubular epithelium, it would ensure efficient recovery of 25(OH)D from the urine and its return to the circulation.

Given this alternative model of vitamin D physiology, because the majority of total serum vitamin D is bound to VDBP, and because VDBP-bound vitamin represents an inert serum reservoir for vitamin storage, although measurement of total 25(OH)D may indicate total body stores, serum concentrations of total 25(OH)D will often not reflect vitamin bioactivity or sufficiency. Non-VDBP bound bioavailable vitamin D, on the other hand, may be a more faithful indicator of vitamin D sufficiency. This model agrees with results from clinical studies described above herein and it provides a model that may explain the differences in 25(OH)D concentrations and differences in BMD between white and black subjects.

Comparing men with osteoporosis to men without osteoporosis, Al-oanzi and colleagues²⁴ found that total 25(OH)D₃ levels were similar in both groups, but VDBP levels were significantly higher (P<0.001) Calculated free 25(OH)D3 and 1,25(OH)₂D3 were significantly lower in men with vs without osteoporosis (p<0.00001).²⁴ Whereas total 25(OH)D3 levels provided only a crude estimate of vitamin D status, measurement of freehormones provided more biologically relevant information. As described herein in Example 1 (young healthy adults; n=49) BMD is not well-correlated with total 25(OH)D but that free and bioavailable 25(OH)D are much more strongly associated with BMD. Despite wide variation in VDBP concentrations in the study cohort, mean VDBP levels were significantly lower in nonwhite than in white subjects (2.87±2.04, 4.94±2.43, respectively; P<0.001). As demonstrated in Example 2 herein, a randomly selected group of racially-matched ESRD patients suggested that VDBP may also mediate vitamin D activity in ESRD. Lower VDBP levels were found in blacks vs whites. Serum calcium correlated with free 25(OH)D and 1,25(OH)₂D, but not with total 25[OH]D and free 25(OH)D and VDBP levels—but not total 25[OH]D—were significantly associated with PTH. As discussed in Example 3 herein, a study in pregnant women also revealed lower VDBP and total 25(OH)D levels in blacks vs whites, whereas bioavailable 25(OH)D was similar regardless of race.

On the basis of the data described herein, it is hypothesized that VDBP modifies the relationship of BMD and 25(OH)D. More specifically, decreased concentrations of VDBP in nonwhites may explain the lower average concentrations of total 25(OH)D that have been consistently reported herein and elsewhere. Because of lower VDBP levels, bioavailable vitamin D will be normal or even increased, perhaps explaining the apparent reduced risk of osteoporosis in blacks compared to whites.

The invention described herein incorporates innovative hypotheses and approaches that: 1. Apply mechanisms of hormone biology that are well-established in other steroid hormone research (e.g. testosterone and thyroid hormones) to explain the biological actions of vitamin D; 2. solves a complex problem that has puzzled clinicians for decades: 3. Is likely to impact the design of future clinical trials in which vitamin D insufficiency is redefined by decreased bioavailable vitamin D levels; 4. Advances the applicability of the 25[OH]D assay that has long been considered the gold-standard for determining vitamin D status and proposes a novel alternative (free/bioavailable D) that may solve perplexing inconsistencies in outcomes in different races that may be secondary to vitamin D status; 5, Advances a contemporary principle that diagnosis and treatment should be individualized based on, at least race and gender, to improve the therapeutic and cost-efficiency of limited health care resources.

Test Hypotheses in HANDLS Subjects.

The hypotheses described below can be explored (FIG. 5) by measuring total 25(OH)D and VDBP levels in stored serum samples from black and white subjects with baseline BMD measurements enrolled in HANDLS:33 1. Blacks have lower levels of VDBP and total 25(OH)D levels, but similar levels of free and bioavailable 25(OH)D as whites. 2. Free and bioavailable 25(OH)D levels are independently associated with BMD in blacks and whites, and are inversely and linearly associated with PTH levels, and the associations are stronger than those between total 25(OH)D and BMD.

Levels of free and bioavailable vitamin D can be calculated from total 25(OH)D. VDBP and serum albumin measurements as shown below.^(38,70,76) Data will be examined using multivariate analyses for the presence of associations between BMD and free- and bioavailable 25(OH)D, and for associations between free- and bioavailable 25(OH)D and PTH in black vs white subjects. Adjustments for covariates such as: history of osteoporosis, age, sex, pre-menopausal status, smoking and alcohol use, oral vitamin D and calcium intake, use of bisphosphonates, exercise, and body mass index can be made.

The HANDLS Study.

The HANDLS study is being conducted as part of the National Institution of Aging Intramural Research Program (NIAIRP). Planned as a 20-year longitudinal study, HANDLS is designed to test hypotheses about aging and health disparities in minority and poor populations by evaluating differences in rates and risks for pathological conditions associated with aging within diverse racial, ethnic, and economic groups. Data on physical, genetic, biologic, demographic, psychosocial, and psychophysiological parameters from a fixed cohort of 3,722 black and white participants in higher and lower socioeconomic status are being collected.

Population being Studied.

HANDLS participants are a fixed cohort of community-dwelling black and white adults aged 30-64. Participants in HANDLS have been recruited from 12 pre-determined neighborhoods (groups of contiguous census tracts) comprising the geographic area of Baltimore city and South Baltimore. The population comprises a 4-way factorial cross of age (seven 5-year age bands between 30-64), sex, race, and socioeconomic status indexed by poverty status.

Variables Available.

The HANDLS database contains information obtained from household interviews of black and white participants about their health status, health service utilization, psychosocial factors, nutrition, neighborhood characteristics, and demographics. In addition, mobile medical research vehicles deployed every three years collect data (over ˜20 years) from the same participants on: medical history and physical examination, dietary recall, cognitive evaluation, psychophysiology assessments including heart rate variability, arterial thickness, carotid ultrasonography, assessments of muscle strength and bone density, and laboratory measurements (blood chemistries, hematology, biomarkers of oxidative stress and biomaterials for genetic studies).

The serum levels of total 25(OH)D, VDBP, albumin, PTH can be examined and bioavailable 25(OH)D calculated in all HANDLS subjects with baseline BMD measurements (˜2200). Associations between VDBP levels, total 25(OH)D, and PTH levels can be tested for. In addition to baseline assessments, 5 follow-up triennial assessments are being collected as part of HANDLS over ˜20 years. At least one follow-up measure at Year 3 (and as many as possible for the duration of the funding period) for an exploratory evaluation of BMD and related outcomes (ie, osteoporosis, fractures).

Blood Available.

Approximately 2,200 participants of HANDLS have baseline BMD measurements and stored serum samples. Followup BMD data, and blood samples collected at Year 3 (and possibly Year 6 as funding allows) can be obtained to evaluate associations between BMD and related outcomes and total, bioavailable, and free 25(OH)D over time.

Analysis Techniques.

Stored serum samples from the HANDLS repository collected at baseline and at Years 3 and 6 (as feasible) can be used. Total 25(OH)D levels can be measured by high performance liquid chromatography/mass spectrophotometry. Albumin can be measured on standard automated platforms. VDBP can be measured using a commercially available ELISA (R&D Systems) as described in Example 1 herein. Interassay CVs and intra-assay CVs for this assay are 5.7% and 7.4% respectively.

In order to validate the calculated estimates of free 25(OH)D and test whether these methods are valid in both black and white subjects, free 25(OH)D can be measured directly in a subset of samples (n=200) as described previously.⁸² Since blood sampling dates are captured, season can be included as a covariate in the modeling of vitamin D measurements.

The PTH assay can be performed using an electrochemiluminescence immunoassay “ECLIA” on the Cobas E601 analyzer (Roche diagnostics). The assay for determining intact PTH employs a sandwich test principle in which a biotinylated monoclonal antibody reacts with the N-terminal fragment (1-37) and a monoclonal antibody labeled with a ruthenium complex reacts with the C-terminal fragment (38-84). The test can performed using 300 μL of EDTA plasma, which provides more stable test results than serum.

Power Calculations.

To determine VDBP, total and bioavailable 25(OH)D, and PTH levels in black vs white subjects. Power was calculated assuming a 2-sided t-test with α=0.05 for differences in black vs white subjects for total 25(OH)D (primary variable of interest). Although no previous studies have explored this measure among different racial groups, bioavailable 25(OH)D is derived from total 25(OH)D and is a secondary variable of interest and it can constitute a reliable proxy. The weighted means and standard deviations were derived from 5 published reports^(18,19,83-85) constituting a total of 14,402 whites and 7,790 blacks with clinical and demographic characteristics similar to what we expect from the HANDLS population (relatively healthy population, predominantly middle-aged). From these studies, an expected mean and standard deviation were derived for total 25(OH)D among whites and blacks (28.07±3.71 ng/mL and 17.88±12.28 ng/mL, respectively). The sample size of nearly 2,200 HANDLS subjects can be expected to be adequate to detect primary and secondary variables of interest with a power of 0.8, even with the possibility of invalid measurements and missing data (estimates at <5% of available observations).

To Test for Associations Between BMD, Bioavailable 25(OH)D, and PTH Compared to Total 25(OH)D in Black Vs White Subjects.

To obtain estimates for whole body BMD, a random sample of 40 subjects, stratified by race, was selected from all available HANDLS subjects with non-missing whole body BMD and total 25(OH)D measurements. Power was calculated assuming a 2-sided p-value with α=0.05. Based on preliminary analysis, r=0.29 between total 25(OH)D and whole body BMD in whites and r=0.24 among blacks was obtained. Assuming a correlation between bioavailable 25(OH)D and whole body BMD to be ˜30% higher, based on findings from the MACS study, 23 the linear relation between these variables can be approximated to be r=0.38 among whites and r=0.31 among blacks. Based on these estimates, the reduced R² among whites and blacks (R²=0.14 and R2=0.10, respectively) for multiple linear regression analyses was calculated. The sample size of nearly 2,200 HANDLS subjects is adequate to detect the primary and secondary variables of interest with a power of 0.8, even with the possibility of invalid measurements and missing data (estimates at <5% of available observations).

Statistical Analysis

Preliminary examination of VDBP, total, bioavailable 25(OH)D, and PTH levels include assessment of the plausibility of values through observed ranges. Measures of central tendency and dispersion can be documented. As initial examination of VDBP, total, bioavailable 25(OH)D, and PTH levels have shown highly, right-skewed distributions, these variables can be assessed for normality through use of visualization techniques such as quantile-quantile plots and testing by Shapiro-Wilkes tests both for the overall sample and stratified by race. If VDBP, total, bioavailable 25(OH)D, and PTH levels are found to be normally distributed, mean levels between black and white subjects can be compared through the use of two-samples t-tests. Otherwise, the distributions between black and white subjects will be compared through the use of nonparametric statistics such as Wilcoxon rank sum tests. Two-tailed p-values of <0.05 will be considered statistically significant.

BMD can be preliminarily be examined for plausibility of values and measures of central tendency and dispersion will be documented. The distribution of BMD can be inspected both through visualization and through formal statistical testing. Exploratory data analysis can be performed through the use of scatterplots to inspect the relationship between BMD, total 25(OH)D, bioavailable 25(OH)D, and PTH. If a linear relationship is found between variables, Pearson Product-Moment Correlation Coefficient or Spearman's Rank Correlation Coefficient (in the case of outliers) can be used to examine associations between BMD, total 25(OH)D, bioavailable 25(OH)D, and PTH. Based on the strength of the relationships found between bioavailable 25(OH)D, total 25(OH)D, and PTH and BMD, multivariable linear regression models can be constructed to determine the independent association of bioavailable 25(OH)D, total 25(OH)D, and PTH to BMD adjusting for other covariates, including history of osteoporosis, age, sex, pre-menopausal status, smoking and alcohol use, oral vitamin D and calcium intake, use of bisphosphonates, exercise, and body mass index. Seasonality can be explored in all models by controlling for month of data collection and if seasonality is found, a cyclic regression curve can be included in the models.

The relationships between covariates and BMD, vitamin D levels, and PTH can be explored through the use of independent samples t-tests (for binary covariates) and simple linear regression (for continuous covariates) as well as through visualization techniques including boxplots and scatterplot matrices. Predictive variables can be selected through the use of Least Angle Regression (LAR)⁸⁶ or Least Absolute Shrinkage and Selection Operator (LASSO)⁸⁷ since both have proved to be more reliable than the traditional stepwise variable selection method. Covariates central to our hypotheses or that have been shown in previous literature to be clinically relevant to 25(OH)D, total 25(OH)D, and PTH and BMD can be left in the models irrespective of selection. Model assessment can be performed through a variety of procedures. Collinearity can be assessed through correlations between covariates and the variance inflation factor (VIF). Residuals can be examined through standardized residual plots and normality can be tested by Shapiro-Wilk tests. Component plus residual plots will provide a means to investigate the linearity between continuous predictors with BMD controlling for the effects of other predictors in the model. The degree of overlap between LOESS curves and the regression line can be used to assess linearity of the predictors. Diagnostics of influential data points can be identified through Cook's distances (D) where observations with (Di>4/n) will be suspected of influence. A jack-knife approach can be used to compare models with and without influential observations and the percentage of error attributed to individual observations can be documented. Observations with high Cook's distances but biologically plausible values can be considered for inclusion in the final models. The final candidates of models can be compared for Akaike Information Criterion (AIC) value as well as adjusted Rsquared value.

Inclusion and formal testing of interactions between all covariates, with special attention paid to the interaction between race and socioeconomic status, can be incorporated into un-stratified multivariable models. Nonsignificant interaction terms can be dropped from final models. Significant interaction terms can be visually inspected through the use of Trellis graphs and the associations between covariates and BMD can be interpreted according to the level of the interactive predictor. Multivariable models cam be conducted stratified by race and will be analyzed in a similar manner with the exclusion of interaction terms including race.

As CVD has been linked to 25(OH)D status, exploratory analyses can be performed using available data to detect any relationships between bioavailable, total 25(OH)D, and PTH and carotid intimal medial thickness and blood pressure at baseline.

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TABLE 1 Characteristics of the Study Population (n = 49). Data are presented as n (%) for categorical variables and mean ± standard deviation for continuous variables. Mean ± SD n (%) Age (years) 23.5 ± 3.4  Body Mass Index (kg/m²) 22.43 ± 2.96  Sex Male 27 (55.1%) Female 22 (44.9%) Race White 31 (63.3%) Non-White 18 (36.7%) Exercise Amount >120 minutes per week 21 (42.9%) ≦120 minutes per week 26 (53.1%) Unknown 2 (4.1%) Vitamin D Binding Protein (umol/L) 4.19 ± 2.49 Albumin (g/L) 42.47 ± 3.94  Serum Calcium (mmol/L) 2.30 ± 0.19 Parathyroid Hormone (ng/L) 29.86 ± 8.25  Dietary Calcium Intake (mg/day) 925.85 ± 421.76 Lumbar Spine Bone Mineral Density (g/cm²) 1.05 ± 0.14

TABLE 2 Serum Levels of Vitamin D. Total 25(OH)D levels were measured along with albumin and vitamin D binding protein (DBP). DBP-bound, albumin-bound, free, and bioavailable 25(OH)D (free and albumin bound) were calculated Mean ± SD Total 25(OH)D (nmol/L) 64.23 ± 27.70 DBP-Bound 25(OH)D (nmol/L) 54.66 ± 26.32 Albumin-Bound 25(OH)D (nmol/L) 9.55 ± 6.72 Free 25(OH)D (pmol/L) 25.37 ± 18.52 Bioavailable 25(OH)D (nmol/L) 9.58 ± 6.74

TABLE 3 Bone Mineral Density, DBP Levels, and 25(OH)D Levels in Select Subgroups. Values are reported as mean ± standard deviation. DBP = vitamin D binding protein. BMD = bone mineral density. OCP = oral contraceptive pill. Groups were compared using t-tests after natural log transformation of total 25(OH)D, DBP, bioavailable 25(OH)D levels and BMD. Total 25(OH)D Total DBP Bioavailable 25(OH)D L-Spine BMD n (nmol/L) (umol/L) (nmol/L) (g/cm²) Sex Male 27 52.79 ± 19.31 3.90 ± 2.09 8.36 ± 5.36 1.04 ± 0.14 Female 22 78.28 ± 30.28 4.53 ± 2.92 11.08 ± 8.01  1.07 ± 0.13 p-value <0.001  0.493 0.113 0.371 OCP Use (Females Only) Yes 7 107.33 ± 27.87  6.27 ± 3.76 12.83 ± 11.64 1.06 ± 0.21 No 15 64.73 ± 20.59 3.71 ± 2.12 10.26 ± 5.98  1.07 ± 0.08 p-value <0.001  0.152 0.841 0.646 Body Mass Index <25 kg/m² 39 66.0 ± 26.9 4.63 ± 2.49 8.59 ± 5.28 1.04 ± 0.12 ≧25 kg/m² 10 57.2 ± 25.0 2.42 ± 1.61 13.43 ± 10.19 1.09 ± 0.19 p-value 0.284 0.003 0.073 0.438 Exercise ≧120 Minutes/Week 21 73.33 ± 26.11 4.14 ± 2.56 11.76 ± 8.35  1.09 ± 0.13 <120 Minutes/Week 26 58.66 ± 27.97 4.20 ± 2.58 8.19 ± 4.85 1.03 ± 0.13 p-value 0.038 0.863 0.089 0.165 Race White 31 68.84 ± 28.65 4.94 ± 2.43 7.84 ± 3.92 1.03 ± 0.10 Non-White 18 56.30 ± 24.76 2.87 ± 2.04 12.56 ± 9.29  1.08 ± 0.18 p-value 0.138 <0.001  0.065 0.346

TABLE 4 Bioavailable 25(OH)D Predicts Bone Mineral Density (BMD). Bioavailable 25(OH)D and BMD were natural log transformed prior to analysis. The coefficient (B) represents the average unit increase in ln BMD for each unit increase in ln bioavailable 25(OH)D. P-value is the statistical significance of the relationship between bioavailable 25(OH)D and BMD after controlling for potential confounders. Thus, the relationship between bioavailable 25(OH)D and BMD remains significant after adjusting for potential confounders. Model B P-value Adjusted R² Bioavailable 25(OH)D 0.092 0.002 0.177 Bioavailable 25(OH)D, 0.072 0.029 0.180 age, sex, race, and BMI

TABLE 5 Characteristics of the population (n = 94) Median (IQR) or n (%) Age, years 65 (50-74) Male 55 (59%) Black race 48 (51%) Survived at least one year on dialysis 47 (50%) Body mass index 25 (22-30) Systolic blood pressure, mm Hg 140 (123-153) Diastolic blood pressure, mm Hg 73 (61-81) Total 25(OH)D, ng/ml 20 (13-28) Total 1,25(OH)₂D, ng/ml 9.5 (5-16) Parathyroid hormone, pg/ml 190 (96-307) Corrected Calcium, mg/dl 8.9 (8.5-9.4) Phosphorus, mg/dl 4.2 (3-5.5) Alkaline phosphatase, mg/dl 82 (66-112.5) Albumin, g/dl 3.4 (3.0-3.8) Vitamin D binding protein, μg/ml 158 (69-217) Bioavailable 25(OH)D, ng/ml 3.4 (2.2-5.0) Bioavailable 1,25(OH)₂D, pg/ml 2.2 (1.1-3.8)

TABLE 6 Race and vitamin D levels. Black individuals had lower total, but not bioavailable, 25(OH)D levels when compared with their white counterparts. Survivors are patients who survived for at least one year after initiating hemodialysis, while non-survivors died within this year. All values represent group medians. Blacks Whites p Total 25(OH)D (ng/ml) 15.1 23.1 <0.001 Bioavailable 25(OH)D (ng/ml) 3.8 2.8 0.21 Total 1,25(OH)₂D (pg/ml) 8 11.5 0.07 Bioavailable 1,25(OH)₂D (pg/ml) 2.2 2.2 0.48 DBP (μg/ml) 75 189 <0.001 Survivors: DBP (μg/ml) 88 195 0.004 Non-survivors: DBP (μg/ml) 58 183 <0.001 PTH (pg/ml) 201 168 0.47

TABLE 7 PTH and bioavailable 25(OH) vitamin D. In univariate and multivariate analyses, bioavailable 25(OH) vitamin D levels were consistently associated with PTH (corresponding p values displayed). PTH and bioavailable vitamin D levels were log transformed prior to analysis, thus β = −0.36 suggests that a 25% increase in bioavailable 25(OH)D is associated with 7.7% decrease in PTH ((1.25^(−0.36) − 1)*100 = −7.7). β p Bioavailable 25(OH)D alone −0.36 0.007 Multivariate model adding age, gender, race −0.33 0.02 Multivariate model with above variables plus survival −0.32 0.02 status at 1 year Multivariate model with above variables plus calcium, −0.39 0.02 phosphorus, bioavailable 1,25(OH)₂D

TABLE 8 Calculation of bioavailable vitamin D levels Number Equation 1 [D_(DBP)] = [Total Vitamin D] − [D_(Alb)] − [D_(free)] 2 [D_(Alb)] = K_(alb) · [Alb] · [D_(free)] 3 [D_(free)] = [D_(DBP)] ÷ K_(DBP) ÷ [DBP_(free)] 4 [DBP_(free)] = [Total DBP] − [D_(DBP)] From equations 3 and 4 5 [D_(free)] = [D_(DBP)] ÷ K_(DBP) ÷ ([Total DBP] − [D_(DBP)]) From equations 1 and 2 6 [D_(DBP)] = [Total Vitamin D] − (K_(alb) · [Alb] + 1) · [D_(free)] 7 [D_(free)] = {[Total Vitamin D] − (K_(alb) · [Alb] + 1) · [D_(free)]} ÷ K_(DBP) ÷ ([Total DBP] − {[Total Vitamin D] − (K_(alb) · [Alb] + 1) · [D_(free)]}) This can be simplified to fit a second-degree polynomial (ax² + bx + c = 0) where x = [D_(free)]: a = K_(DBP) · K_(alb) · [Alb] + K_(DBP) b = K_(DBP) · [Total DBP] − K_(DBP) · [Total Vitamin D] + K_(alb) · [Alb] + 1 c = −[Total Vitamin D] 8 [D_(free)] = [−b + √b2 − 4ac] ÷ 2a 9 [D_(bioavailable)] = [D_(free)] + [D_(Alb)] = (K_(alb) · [Alb] + 1) · [D_(free)] [Total Vitamin D] = total measured vitamin D concentration (either 25-OH or 1,25-(OH)₂ vitamin D) [Alb] = measured albumin concentration [Total DBP] = measured vitamin D binding protein concentration [D_(Alb)] = concentration of albumin-bound vitamin D [D_(DBP)] = concentration of DBP-bound vitamin D [D_(free)] = concentration of free (unbound) D [D_(bioavailable)] = concentration of Bioavailable D = [D_(free)] + [D_(Alb)] K_(alb) = affinity constant between vitamin D and albumin = 6 × 10⁵ M⁻¹ (for 25-OH D) or 5.4 × 10⁴ M⁻¹ (for 1,25-(OH)₂ D) K_(DBP) = affinity constant between vitamin D and DBF = 7 × 10⁸ M⁻¹ (for 25-OH D) or 3.7 × 10⁷ M⁻¹ (for 1,25-(OH)₂ D)

TABLE 9 Comparison of 25(OH)D insufficiency in blacks vs. whites based on current definitions % 25(OH)D Deficient 25(OH)D Population Age (years) Blacks Whites Cutoff Levels Reference NHANES 2001-2006 >45 (82-85%) 80 40 <20 ng/mL Diaz⁵¹ Older men (MrOS) >65 65 23 <20 ng/mL Orwoll¹⁷ 22 2 <10 ng/mL Hemodialysis 63 ± 15 31 12 <10 ng/mL Wolf⁴³ patients (ArMORR) Men in BACH/Bone 30-79 44 11 <21 ng/mL Hannan¹⁹ Survey NHANES = National Health and Nutrition Examination Survey; MrOS = Osteoporotic Fractures in Men Study; ArMORR = Accelerated Mortality on Renal Replacement; BACH = Boston Area Community Health

Example 5: VDBP Polymorphisms

Vitamin D binding protein (VDBP) is the primary vitamin D carrier protein, binding 85-90% of total circulating 25(OH)D (Bikle et al., J Clin Endocrinol Metab 1986; 63:954-9). VDBP appears to inhibit some actions of vitamin D, as the bound fraction may be unavailable to exert biological actions on target cells (Safadi et al., J Clin Invest 1999; 103:239-51; Chun et al., J Clin Endocrinol Metab 2010; 95:3368-76; Bikle and Gee, Endocrinology 1989; 124:649-54). Common genetic polymorphisms in the VDBP gene track with race (Engelman et al., J Clin Endocrinol Metab 2008; 93:3381-8; Constans et al., Am J Phys Anthropol 1985:68:107-22; Lauridsen et al., Calcif Tissue Int 2005; 77:15-22; Lauridsen et al., Clin Chem 2001; 47:753-6.) and produce variant VDBP proteins, which differ in affinity for vitamin D (Chun et al., J Clin Endocrinol Metab 2010; 95:3368-76; Arnaud et al., Hum Genet 1993; 92:183-8; Braun et al., Hum Genet 1992; 89:401-6). Clinical assays presently measure total 25(OH)D without distinguishing fractions bound to major carrier proteins.

We hypothesized that VDBP genotypes might affect circulating VDBP concentrations and thus account for observed racial differences in manifestations of vitamin D deficiency.

Participants in the HANDLS study as described in Example 4, were genotyped for two common single nucleotide polymorphisms in the VDBP gene (rs4588 and rs7041). See the supplementary appendix for detailed methods. We successfully genotyped 1999 participants.

Methods

Study Population

Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) is a population-based cohort study supported by the Intramural Research Program of the National Institute on Aging, National Institutes of Health (N=3720). Study participants were age 30 to 64 years, lived in Baltimore, Md., and were recruited from 13 contiguous U.S. Census tracts. Participants were randomly sampled from within age, race, gender, and socioeconomic status strata, excluding those who did not self-identify as black or white. The Medstar Research Institute's Institutional Review Board approved the protocol. The Partners Committee on Human Research exempted the present study from review.

Data Collection

We used cross-sectional data from HANDLS collected between 2004 and 2008. After a home-based interview, participants underwent an examination on a mobile research vehicle where blood was sampled, height and weight measured, and bone densitometry performed. Only those who completed the examination, including bone densitometry (restricted to weight less than 270 pounds), and who had sufficient blood samples available were included in the present study (N=2085). Bone densitometry was performed using the Lunar DPX-IQ (Lunar Corp., Madison, Wis.). Femoral neck bone mineral density was examined in detail given its clinical relevance as a risk factor for hip fracture.

Laboratory Analysis

Blood samples drawn at the examination were frozen for future analysis. Total 25(OH)D₂ and 25(OH)D₃ levels were measured using tandem mass spectrometry (inter-assay CV 8.6%; Schottker et al., PLoS One 2012; 7:e48774). VDBP levels were measured using a commercial enzyme-linked immunosorbant assay (R&D Systems, Minneapolis, Minn., inter-assay CV 15%). Intact parathyroid hormone levels were measured using the Cobas electrochemiluminescense immunoassay on the Modular Analytics E170 automated analyzer (Roche Diagnostics, Indianapolis, Ind., USA; inter-assay CV 2.5%). Calcium levels were corrected for albumin (serum calcium+0.8*[4-serum albumin]).

Genotyping

Participants were genotyped for two common single nucleotide polymorphisms in the VDBP gene (rs4588 and rs7041).

VDBP Single Nucleotide Polymorphism Genotyping

Samples were genotyped for two common single nucleotide polymorphisms in the VDBP gene (rs4588 and rs7041). All samples were genotyped using the ABI PRISM 7900HT Sequence Detection System (Applied Biosystems, Foster City, Calif.), in 384-well format. The 5′ nuclease assay (TaqMan®) was used to distinguish the 2 alleles of a gene. PCR amplification was carried out on 5-20 ng DNA using 1× TaqMan® universal PCR master mix (No Amp-erase UNG) in a 5 μl reaction volume. Amplification conditions on an AB 9700 dual plate thermal cycler (Applied Biosystems, Foster City, Calif.) were as follows: 1 cycle of 95° C. for 10 min, followed by 50 cycles of 92° C. for 15 s and 60° C. for 1 min. TaqMan® assays were ordered using the ABI Assays-on-Demand service. The success rate for genotyping was 95.8%.

HANDLS Whole Genome Sequencing and Ancestry Estimates

Participants were successfully genotyped to 907763 SNPS at the equivalent of Illumina 1M SNP coverage (709 samples using Illumina 1M and 1Mduo arrays, the remainder using a combination of 550K, 370K, 510S and 240S to equate the million SNP level of coverage), passing inclusion criteria into the genetic component of the study. Initial inclusion criteria for genetic data in HANDLS includes concordance between self reported sex and sex estimated from X chromosome heterogeneity, >95% call rate per participant (across all equivalent arrays), concordance between self-reported African ancestry and ancestry confirmed by analyses of genotyped SNPs, and no cryptic relatedness to any other samples at a level of proportional sharing of genotypes >15% (effectively excluding 1^(st) cousins and closer relatives from the set of probands used in analyses). In addition, SNPs were filtered for HWE p-value>1e-7, missing by haplotype p-values >1e-7, minor allele frequency >0.01, and call rate >95%. Basic genotype quality control and data management was conducted using PLINKv1.06 (PMID: 17701901). Cryptic relatedness was estimated via pairwise identity by descent analyses in PLINK and confirmed using RELPAIR (PMID: 11032786).

Ancestry estimates were assessed using both STRUCTUREv2.3 (PMID: 10835412, PMID: 12930761, PMID: 18784791) and the multidimensional scaling (MDS) function in PLINKv1.06. In the multidimensional scaling analysis, HANDLS participants were clustered with data made available from HapMap Phase 3 for the YRI, ASW, CEU, TSI, JPT and CHB populations, using a set of 36892 linkage-disequilibrium-pruned SNPs common to each population. This set of SNPs were chosen as they are not in r²>0.20 with another SNP in overlapping sliding windows of 100 SNPs in the ASW samples. HANDLS participants with component vector estimates consistent with the HapMap ASW samples for the first 4 component vectors were included. In addition, the 1024 quality controlled HANDLS samples were later clustered among themselves using MDS to generate 10 component vectors estimating internal population structure within the HANDLS study. Of the SNPs utilized for MDS clustering, the 2000 SNPs with the most divergent allele frequency estimates between African populations (frequency estimates based on YRI samples) and European populations (frequency estimates based on combined CEU and TSI samples) were utilized as ancestry informative markers (AIMs). These 2000 AIMs were associated with frequency differences on the level of p-values <1e-3 based on chi-squared tests. A two population model in STRUCTURE was used to estimate percent African and percent European ancestry in the HANDLS samples, for a 10000 iteration burn-in period, and a 10000 iteration follow-up of the Markov Chain Monte Carlo model utilized by STRUCTURE. The ancestry estimates from STRUCTURE were highly concordant with the first component vector of the MDS clustering of HANDLS samples, with an r² of >0.82.

HANDLS participant genotypes were imputed using MACH and miniMac based on combined haplotype data for HapMap Phase 2 YRI and CEU samples that includes monomorphic SNPs in either of the two constituent populations (release 22, build 36.3). This process followed two stages, first estimating recombination and crossover events in a random sample of 200 participants, then based on this data and the reference haplotypes, 200 iterations of the maximum likelihood model were used to estimate genotype dosages for imputed SNPs. After filtering based on a minimum imputation quality of 0.30, indicated by the RSQR estimate in MACH, with a total yield of 2939993 SNPs (note, this data sent to you has been filtered for RSQR>0.3 and MAF>0.01). Genotype clusters are available for SNPs genotyped in HANDLS upon request. Data imputed to the entire phase 1 alpha version 3 data freeze of the 1000 Genomes Project is available for analyses upon request.

We successfully genotyped 1999 participants.

Calculation of Bioavailable 25(OH) D Levels

Bioavailable 25(OH)D was defined as the circulating 25(OH)D not bound to VDBP, analogous to bioavailable testosterone (Vermeulen et al., J Clin Endocrinol Metab 1999; 84:3666-72). Bioavailable 25(OH)D was calculated in subjects homozygous at both rs7041 and rs4588 (N=1033), for whom we could use a single genotype-specific binding affinity constant, as follows (see also Arnaud et al., Hum Genet 1993; 92:183-8):

Definitions

D=25-hydroxyvitamin D (calcidiol), sum of both D2 and D3

Alb=albumin

DBP_(1S)=Gc1S variant of the Vitamin D binding protein, as encoded by the GC gene containing the rs7041 single nucleotide polymorphisms, with a T>G substitution resulting in the substitution of Aspartic acid with glutamic acid at residue 416 of the VDBP polypeptide. The rs4588 single nucleotide polymorphism for Gc1S (C) is the ancestral allele encoding threonine at position 420.

DBP_(1F)=Gc1F variant of the Vitamin D binding protein, as encoded by the GC gene containing the ancestral alleles for both rs7041 and rs4588 single nucleotide polymorphisms; these alleles encode for aspartic acid and threonine at positions 416 and 420 of the VDBP polypeptide.

DBP₂=Gc2 variant of the Vitamin D binding protein, as encoded by the GC gene containing the rs4588 SNP, with a C>A substitution resulting in the substitution of threonine acid with lysine at residue 420 of the VDBP polypeptide. The rs7041 single nucleotide polymorphism for Gc2 is the ancestral allele (T) encoding aspartic acid at position 416.

DBP_(1S)=Gc1S variant of the Vitamin D binding protein, as encoded by the GC gene containing the rs7041 SNP, with a T>G substitution resulting in the substitution of Aspartic acid with glutamic acid at residue 416 of the VDBP polypeptide.

-   -   [D_(Alb)]=concentration of albumin-bound vitamin D     -   [D_(DBP)]=concentration of DBP-bound vitamin D     -   [D]=concentration of free (unbound) D     -   [Total]=concentration of Total 250H-D=[D_(DBP)]+[D_(Alb)]+[D]     -   [Bio]=concentration of Bioavailable D (Bioavailable=sum of free         and albumin-bound vitamin)=[D]+[D_(Alb)]     -   K_(alb)=affinity constant between vitamin D and albumin=6×10⁵         M⁻¹     -   KDBP_(generic)=genotype-nonspecific affinity constant between         25-hydroxyvitamin D and DBP=0.7×10⁹ M⁻¹     -   KDBP_(1S)=affinity constant between vitamin D and         DBP_(1S)=0.6×10⁹ M⁻¹     -   KDBP_(1F)=affinity constant between vitamin D and         DBP_(1F)=1.12×10⁹ M⁻¹     -   KDBP₂=affinity constant between vitamin D and DBP₂=0.36×10⁹ M⁻

Equations

Total 25(OH)-Vitamin D [Total]=concentration of 25(OH)-Vitamin D in g/mol÷400.5 g/mole Given that [Total]=[D]+[D _(Alb) ]+[D _(DBP)] thus [D _(DBP)]=[Total]−[D _(Alb) ]−[D]  (Eq. 1)

Albumin [Alb]=serum albumin concentration in g/L÷66,430 g/mole [D]+[Alb]·[D _(Alb)] Albumin association constant K _(alb) =[D _(Alb)]÷([D]·[Alb]) Thus [D _(Alb) ]=K _(alb)·[Alb]·[D]  (Eq. 2)

-   -   (NB: [Alb] in this example denotes the concentration of free         non-vitamin bound albumin. However, given the low affinity         between albumin and Vit. D, the concentrations of total albumin         and unbound albumin are effectively equivalent ([Total         Albumin]≈[Alb]). As a result, [Alb] may be estimated accurately         by measurements of total serum albumin.)

DBP [Total DBP]=concentration of serum DBP in g/L÷58,000 g/mole [DBP]=free unbound DBP and [D _(DBP)]=vitamin-bound DBP Given that [D]+[DBP]

[D _(DBP)] And DBP association constant K _(DBP) =[D _(DBP)]÷([DBP]·[D]) Thus [D]=[D _(DBP) ]÷K _(DBP)÷[DBP]  (Eq. 3) Since [Total DBP]=sum of bound and unbound DBP=[DBP]+[D _(DBP)] Therefore [DBP]=[Total DBP]−[D _(DBP)]  (Eq. 4)

Solving for Free 25(OH)-Vitamin D

From Eqs. 3 and 4 we see that: [D]=[D _(DBP) ]÷K _(DBP)÷([Total DBP]−[D _(DBP)])  (Eq. 5)

If we substitute Eq. 1 into Eq. 2, we find that: [D _(DBP)]=[Total]−(K _(alb)·[Alb]+1)·[D]  (Eq. 6)

Substituting Eq. 6 into Eq. 5 produces the following: [D]=([Total]−(K _(alb)·[Alb]+1)·[D])÷K _(DBP)÷([Total DBP]−([Total]−(K _(alb)·[Alb]+1)·[D])) The equation is now limited to known constants (K_(DBP) and K_(alb)), measured values ([Total DBP], [Alb], and [Total]) and the dependent variable for free vitamin D [D]. After propagating products and several rearrangements we can further simplify this to fit the form of a second-degree polynomial: ax ² +bx+c=0

-   -   Where x=[D]=the concentration of free 25(OH)-Vitamin D         a=K _(DBP) ·K _(alb)·[Alb]+K _(DBP)         b=K _(DBP)·[Total DBP]−K _(DBP)·[Total]+K _(alb)·[Alb]+1         c=−[Total]     -   This polynomial may be solved for [D] using the quadratic         equation:

$\lbrack D\rbrack = \frac{{- b} + \sqrt{b^{2} - {4a\; c}}}{2a}$

-   -   After solving for free 25(OH)-vitamin D, we may then use Eq. 2         to calculate the concentration of bioavailable (non-DBP bound         vitamin):         [Bio]=[D]+[D _(alb)]=(K _(alb)·[Alb]+1)·[D]  (Eq. 7)     -   Furthermore, if the DBP genotype for an individual patient is         known, for patients who are homozygous for Gc1S/Gc1S, Gc1F/Gc1F,         or Gc2/Gc2, the genotype-adjusted free and bioavailable         fractions of 25-hydroxyvitamin D can be calculated using the         known binding affinities for the three variants (ref. 34):     -   For subjects homozygous for Gc1F variant, K_(DBP)=1.12×10⁸M⁻¹     -   For subjects homozygous for Gc1S variant, K_(DBP)=0.60×10⁸M⁻¹     -   For subjects homozygous for Gc2 variant, K_(DBP)=0.36×10⁸M⁻¹

Example Calculations

For a patient with a known VDBP genotype indicating homozygosity for Gc1F/Gc1F: Total 25(OH)-vitamin D=[Total]=40 ng/mL=1.0×10⁻⁷ mol/L Total serum DBP=[Total DBP]=250 ug/mL=4.3×10⁻⁶ mol/L Total serum albumin=[Alb]=4.3 g/dL=6.4×10⁻⁴ mol/L K _(alb)=6×10⁵ M⁻¹ K _(DBP)=1.12×10⁸M⁻¹ a=4.36×10¹¹ b=5147 c=−1×10⁻⁷ Calculated concentration of free 25(OH)D=1.94×10⁻¹¹ mol/L=7.8 pg/mL Calculated concentration of bioavailable 25(OH)D=7.54×10⁻⁹ mol/L=3.0 ng/mL

Genotype-specific calculated bioavailable 25-hydroxyvitamin D concentrations were validated by directly measuring non-VDBP-bound 25-hydroxyvitamin D in a subset of homozygous subjects using a competitive radioligand binding assay (see Example 5).

Statistical Analysis

Race-stratified participant characteristics are presented as means±standard errors or number (percent) and compared using t-tests for continuous variables and chi-square tests for categorical variables. Non-normally distributed variables were natural log transformed to meet assumptions of parametric testing. Adjusted means and standard errors were derived from multiple linear regression models containing terms for age, sex, body mass index, poverty status, season, smoking status, and calcium intake. For models examining racial differences, interactions between race and the main predictor of interest were included as covariates.

Subjects were divided into quintiles to examine relationships between 25(OH)D measures and plasma parathyroid hormone, serum calcium, and bone mineral density. For quintile analyses, P-values are presented from both categorical and continuous models. R-squared values for models exploring variation in total 25(OH)D and VDBP levels were derived from semi-partial correlation coefficients using Type I sums of squares from multiple linear regression models.

Chi-squared tests were used to compare allele frequencies in blacks and whites. Unadjusted, race-stratified, additive effects models were used to summarize associations between VDBP and 25(OH)D levels and the two single nucleotide polymorphisms of interest (rs7041 and rs4588). In a subset of 783 samples from black participants with complete data from Genome-Wide Association Studies, identical statistical models were rerun using 10 principal components or genome-wide percent African ancestry estimates as covariates. The parameters adjusting for population substructure were not significant and made little impact on the model. Therefore, we did not include these covariates in reported models.

Statistical analyses were conducted in SAS version 9.2. Two-tailed P-values of less than 0.05 were considered significant with the exception of genotype analysis where p-values were adjusted for the presence of 2 SNPs (P<0.025).

Results

Participant Characteristics

Black (N=1181) and white (N=904) participants were similar in age, sex, body mass index, and female menopausal status (Table 10). Blacks were more likely than whites to be impoverished, active smokers, or have microalbuminuria. Use of hormone replacement therapy and medications that affect vitamin D metabolism was uncommon.

TABLE 10 Characteristics of Community-Dwelling Blackand White American Participants. Overall Black White Characteristic (N = 2,085) (N = 1,181) (N = 904) P-value Male - no. (%) 921 (44.2) 523 (44.3) 398 (44.0) 0.91 Age (years) 48.3 ± 0.2 48.3 ± 0.3 48.3 ± 0.3 0.92 Below Poverty Line - no. (%) 850 (40.8) 573 (48.5) 277 (30.6)  <0.001* Body Mass Index (kg/m²) 29.6 ± 0.2 29.4 ± 0.2 29.8 ± 0.2 0.14 Houston Activity Scale†  2.4 ± 0.1  2.2 ± 0.1  2.8 ± 0.1  <0.001* Current Smoker - no. (%) 930 (44.6) 552 (46.7) 378 (41.8)  0.01* Hx of Osteoporosis - no. (%) 51 (2.5) 19 (1.6) 32 (3.5)  0.01* Prescribed Osteoperosis Therapies - 29 (1.4) 10 (0.9) 19 (2.1)  0.02* no. (%)†† Post-Menopausal - no. (%) of 823 (53.8) 345 (52.8) 278 (55.1) 0.42 Females HRT - no. (%) of Females 27 (2.4) 10 (1.6) 17 (3.5)  0.045* Urine Microalbumin > 30 (mg/dl)- no. 37 (1.8) 27 (2.3) 10 (1.1)  0.01* (%) eGFR by CKD-EPI < 60 (mL/min/1.73 114 (5.5)  67 (5.7) 47 (5.2) 0.53 m²) - no. (%) Prescribed Anti-Epileptics - no. (%)†† 14 (0.7)  6 (0.5)  8 (0.9) 0.30 Prescribed Corticosteroids - no. (%)†† 28 (13)  20 (1.7)  8 (0.9) 0.11 Vitamin D Intake (IU/day) 152 ± 4  149 ± 5  157 ± 6  0.38 Calcium Intake (mg/day) 731 ± 11 720 ± 14 744 ± 17 0.10 Hx = History, HRT = Hormone Replacement Therapy, eGFR = Estimated Glomerular Filtration Rate †One-thousand, four-hundred, and fifty-seven participants had missing data (69.9%) ††Anti-epileptics include: Phenobarbital, Carbamazepine, Phenytoin, Primidone; Corticosteroids include: Prednisone, Hydrocortisone, Methylprendisolone, Prednisolone, Dexamethasone; Osteoperosis therapies include: Pamidronate, Neridronate, Olpadronate, Alendronate, Ibandronate, Risedronate, Zoledronate, Denosumab, Teraparatide, and Raloxifene *Significant at P < 0.05

Total 25(OH) D and VDBP Levels

Unadjusted total 25(OH)D levels were lower in blacks compared to whites (15.6±0.2 ng per ml versus 25.8±0.4 ng per ml, P<0.001). Racial differences in total 25(OH)D levels persisted after multivariate adjustment, including adjustment for microalbuminuria (17.3±0.3 ng per ml in blacks versus 25.5±±0.4 ng per ml in whites, P<0.001). There were seasonal differences in 25(OH)D (Table 11). In a model without the genetic polymorphisms of interest, race explained 16.3% of the variation in total 25(OH)D levels.

Unadjusted VDBP levels were lower in black compared to whites (168±3 versus 337±5 μg/mL, P<0.001). Racial differences in VDBP persisted after multivariate adjustment, including adjustment for microalbuminuria, (169±5 in blacks versus 337±5 in whites, P<0.001). There were seasonal differences in VDBP levels (Table 11). In a model without genetic polymorphisms of interest, race explained 30.2% of the variation in VDBP levels.

TABLE 11 Seasonal Differences Summer Fall Spring Winter Blacks no. (%) 182 (15.4) 321 (27.2) 353 (29.9) 325 (27.5) Total 25(OH)D (ng/ml) 19.0 ± 0.6** 18.1 ± 0.4** 13.2 ± 0.4 13.8 ± 0.4 VDBP (μg/ml) 173 ± 9   167 ± 6    153 ± 6** 183 ± 6  PTH (pg/ml) 35.8 ± 1.0** 36.3 ± 1.0** 40.7 ± 1.0 41.6 ± 1.0 Calcium (mg/dl)  9.13 ± 0.03** 9.14 ± 0.2**   9.3 ± 0.02**  9.04 ± 0.02 Whites no. (%) 223 (24.7) 278 (30.8) 202 (22.4) 201 (22.2) Total 25(OH)D (ng/ml) 30.5 ± 0.7** 27.4 ± 0.6** 22.1 ± 0.7 22.0 ± 0.7 VDBP (μg/ml) 353 ± 9*  324 ± 9    353 ± 10* 322 ± 10 PTH (pg/ml) 32.9 ± 1.0  33.7 ± 1.0  34.1 ± 1.0 34.0 ± 1.0 Calcium (mg/dl) 9.00 ± 0.02  9.02 ± 0.02*  8.97 ± 0.02  8.94 ± 0.02 25(OH)D = 25-hydroxyvitamin D, VDBP = Vitamin D Binding Protein, PTH = Parathyroid Hormone *Significantly different from winter at P < 0.05, **Significantly different from winter at P < 0.01, †Corrected for albumin

VDBP Genetic Polymorphisms

At rs7041, blacks were more likely to have the A allele, while whites were more likely to have the C allele (A allele frequency-0.83 in blacks versus 0.42 in whites, P<0.001). Blacks were less likely to have the T allele at rs4588 compared to whites (T allele frequency=0.10 in blacks versus 0.28 in whites P<0.001). No subjects had both the C allele at rs7041 and T allele at rs4588.

The A allele at rs7041 resulted in low levels of VDBP in both black and white Americans (Table 12). The T at rs4588 resulted in higher VDBP in both blacks and whites, after accounting for the observation that all of these subjects had the A allele at rs7041. The polymorphisms at rs7041 and rs4588 both showed dose-dependent effects on VDBP concentrations, with heterozygous subjects showing VDBP concentrations intermediate between that of the homozygotes (Table 12). Genetic variants independently explained 79% of variation in VDBP levels after accounting for other factors. After accounting for genetic variants, race explained less than 1% of variation in VDBP levels.

The A allele at rs7041 was associated with low total 25(OH)D levels among blacks. In whites, the T allele at rs4588 was associated with lower total 25(OH)D levels (Table 12). Rs7041 and rs4588 polymorphisms explained 10.0% of variation in total 25(OH)D levels after accounting for other factors. In the same model, season, race, and body mass index explained 13.5%, 7.3%, and 1.4% of variation in total 25(OH)D levels respectively. Sex, age, smoking, calcium intake, body mass index, and microalbuminuria each explained less than 2% of variation. Overall 30.2% of variation was explained in a model containing the aforementioned variables. VDBP concentration independently explained a similar amount of variation as VDBP genotype.

TABLE 12 Influence of Genetic Polymorphisms on Vitamin D Binding Protein and Total 25-Hydroxyvitamin D Levels Change in Total Change in 25(OH)D VDBP level level per Variant per variant variant Reference Variant Allele allele copy allele copy Race SNP Allele Allele Frequency N (95% CI) P-value (95% CI) P-value Black rs7041 C A 0.83 1,137 −189.4 (−195.6, <0.0001* −1.9 (−2.8, <0.0001* −183.1) ug/ml −1.0) ng/ml rs4588 G T 0.10 57.2 (49.5, <0.0001* −0.6 (−1.7, 0.29 64.9) ug/ml 0.5) ng/ml White rs7041 C A 0.42 862 −189.1 (−201.0, <0.0001* 0.2 (−1.3, 0.80 −177.2) ug/ml 1.7) ng/ml rs4588 G T 0.28 49.9 (36.9, <0.0001* −2.5 (−4.1, 0.002* 62.98) ug /ml −0.9) ng/ml 25(OH)D = Total 25-hydroxyvitamin D, VDBP = Vitamin D Binding Protein Significant at P < 0.025 (adjusted for 2 SNPs)

Bioavailable 25(OH)D in Homozygous Subjects

FIG. 9A shows the percentage of homozygous participants in each racial group with each variant VDBP protein (resulting from unique combinations of the rs7041 and rs4588 polymorphisms). We calculated the concentrations of bioavailable 25(OH)D based upon plasma concentrations of total 25(OH)D, VDBP, and the specific 25(OH)D binding affinity of each VDBP variant. Estimated bioavailable 25(OH)D levels were similar in 1033 black and white homozygous subjects (2.9±0.1 ng/ml in blacks versus 3.1±0.1 ng/ml in whites, P=0.71, FIG. 9B).

Levels of 25(OH)D and Markers of Vitamin D Status

Adjusted mean femoral neck bone mineral density was greater in blacks than in whites (1.05±0.01 versus 0.94±0.01 g/cm², P<0.001), as were adjusted mean calcium levels (9.11±0.01 versus 8.99±0.01 mg/dl, P<0.001). Femoral neck bone mineral density was not associated with bioavailable or total 25(OH)D in black participants; however, in whites, bone mineral density increased with increasing total or bioavailable 25(OH)D levels (Table 13). Calcium levels increased with increasing total 25(OH)D in blacks only (Table 13).

Adjusted mean levels of parathyroid hormone were greater in blacks than in whites (39±1 pg/mL versus 34±1, P<0.001). Lower total or bioavailable 25(OH)D levels were associated with higher levels of parathyroid hormone in both races (Table 13). When compared to whites with similar parathyroid hormone levels, blacks had total 25(OH)D levels that were significantly lower. In contrast, homozygous black and white Americans with similar parathyroid hormone levels had similar bioavailable 25(OH)D levels.

TABLE 13 Total and Bioavailable 25(OH)D and Markers of Vitamin D Sufficiency in Black and White Americans Total Bioavailable 25(OH) D BMD PTH Calcium 25(OH) D BMD PTH Calcium Quintile Mean ± Mean ± Mean ± Quintile Mean ± Mean ± Mean ± (Min-Max) N SE^(†) SE^(†) SE^(†) (Min-Max) N SE^(†) SE^(†) SE^(†) Black Black 1 (0-10) 357 1.05 ± 43.3 ± 9.08 ± 1 (0.00-1.40) 131 1.03 ± 44.3 ± 9.07± 0.01 1.0 0.02 0.02 1.0 0.03 2 (11-15) 324 1.06 ± 38.1 ± 9.08 ± 2 (1.41-1.99) 138 1.05 ± 41.4 ± 9.09 ± 0.01 1.0 0.02 0.01 1.0 0.03 3 (16-20) 221 1.05 ± 36.8 ± 9.14 ± 3 (2.00-2.77) 112 1.05 ± 38.1 ± 9.17 ± 0.01 1.0 0.03 0.02 1.0 0.04 4 (21-28) 193 1.05 ± 36.5 ± 9.10 ± 4 (2.78-4.24) 139 1.03 ± 36.2 ± 9.11 ± 0.01 1.0 0.03 0.01 1.0 0.03 5 (29-90)  86 1.03 ± 33.1 ± 9.21 ± 5 (4.25-15.72) 126 1.06 ± 34.1 ± 9.11 ± 0.02 1.1 0.04 0.02 1.0 0.04 P-value for Trend 0.53 <0.001* 0.02* P-value for Trend 0.53 <0.001* 0.34 White White 1 (0-10)  53 0.92 ± 41.5 ± 8.95 ± 1 (0.00-1.40) 71 0.88 ± 39.3 ± 9.06 ± 0.02 1.1 0.05 0.02 1.0 0.04 2 (11-15) 101 0.90 ± 38.2 ± 8.99 ± 2 (1.41-1.99) 65 0.92 ± 35.4 ± 898± 0.02 1.0 0.03 0.02 1.0 0.04 3 (16-20) 165 0.92 ± 35.9 ± 9.00 ± 3 (2.00-2.77) 90 0.97 ± 32.5 ± 9.00 ± 0.01 1.0 0.03 0.02 1.0 0.03 4 (21-28) 245 0.94 ± 32.7 ± 8.96 ± 4 (2.78-4.24) 64 0.97 ± 29.6 ± 9.03 ± 0.01 1.0 0.02 0.02 1.0 0.04 5 (29-90) 340 0.96 ± 30.9 ± 9.01 ± 5 (4.25-15.72) 76 0.95 ± 29.7 ± 9.02 ± 0.01 1.0 0.02 0.02 1.0 0.04 P-value for Trend 0.003* <0.001* 0.40 P-value for Trend 0.007* <0.001* 0.83 BMD = Bone Mineral Density, PTH = Parathyroid Hormone *Significant at p < 0.05 ^(†)Adjusted for age, season, sex, body mass index, smoking status, socioeconomic status, and calcium intake (except where calcium is the outcome)

Total 25(OH)D levels are partially genetically determined (Engelman et al., J Clin Endocrinol Metab 2008; 93:3381-8; Hunter et al., J Bone Miner Res 2001; 16:371-8). In the present study, genetic polymorphisms in VDBP explained a greater proportion of variation in total 25(OH)D than genetic variants identified in a recent genome wide association study (Wang et al., Lancet 2010; 376:180-8) and a greater proportion of variation than most factors known to be associated with vitamin D levels. To our knowledge, this is the largest study of VDBP polymorphisms in a black American population (Wang et al., Lancet 2010; 376:180-8; Carpenter et al., J Bone Miner Res 2012; et al., Am J Clin Nutr 2009; 89:634-40; Fang et al., Calcif Tissue Int 2009; 85:85-93; Al-oanzi et al., Osteoporos Int 2008; 19:951-60). VDBP only partially explained racial differences total 25(OH)D levels; other factors, including skin pigmentation, contribute to lower total 25(OH)D levels in blacks (Aloia et al., Am J Clin Nutr 2008; 88:545S-50S; Harris S S, Dawson-Hughes et al., J Clin Endocrinol Metab 2007; 92:3155-7; Clemens et al., Lancet 1982; 1:74-6; Bell et al., J Clin Invest 1985; 76:470-3). The effect of VDBP polymorphisms on total 25(OH)D concentrations was likely mediated through VDBP concentration, as VDBP levels explained a similar amount of variation as the VDBP polymorphisms. Though the VDBP-null mice require less total circulating 25(OH)D for sufficiency, they are more susceptible to vitamin D deficiency when deprived of vitamin D; VDBP serves as a 25(OH)D reservoir and aids in the reabsorption of filtered vitamin D through megalin in the kidney (Safadi et al., J Clin Invest 1999; 103:239-51; Nykjaer et al., Cell 1999; 96:507-15). We speculate that low VDBP levels may predispose to vitamin D deficiency when vitamin D sources are scarce.

Currently, screening for vitamin D deficiency with total 25(OH)D levels is widespread. Black Americans are frequently classified as vitamin D deficient and are supplemented with exogenous vitamin D. Vitamin D deficiency is certainly present in those individuals with low total 25(OH)D levels accompanied by hyperparathyroidism, hypocalcemia, or low bone mineral density. However, community dwelling blacks whose total 25(OH)D levels are below the threshold used to define vitamin D deficiency typically lack the physiologic alterations observed in this condition. The high prevalence of a polymorphism in the VDBP gene associated with low VDBP among blacks maintains similar bioavailable 25(OH)D levels to whites despite lower total 25(OH)D levels (FIG. 9C). Alterations in VDBP levels may therefore be responsible for observed racial differences in total 25(OH)D levels and manifestations of vitamin D deficiency. Improved assessment of vitamin D status in diverse populations will require accounting for VDBP.

Example 6: Validation of Calculated Bioavailable 25(OH)D Measurements Compared to Direct Measurement of Bioavailable 25(OH)D Using a 25-Hydroxyvitamin D Radioligand Competitive Binding Assay (VRCBA)

This example describes a differential affinity precipitation method, which was used to directly measure non-VDBP-bound 25-hydroxyvitamin D. Genotype-specific calculated bioavailable 25-hydroxyvitamin D concentrations as described in Example 5, above, were validated using this method in a subset of homozygous subjects using a competitive radioligand binding assay. Measured and calculated 25-hydroxyvitamin D were correlated (In 13 Gc1S homozygotes: R=0.81, in 33 Gc1F homozygotes: R=0.89, P<0.001 for both, FIGS. 10-12).

Materials

25(OH)D affinity adsorption plates were made using Costar 96-well flat bottom EIA plates. Wells were first coated with purified Vitamin D Binding Protein (Gc globulin from human plasma, >90% pure, Sigma Aldrich). Each well was treated with 1 microgram of Gc globulin diluted into 100 microliters of water and allowed to adsorb at 4° C. overnight. Wells were then washed with water and blocked with 500 microliters human serum albumin diluted in water (1% w/v). Plates were stored at 4° C. until use, at which time blocking solution was washed away with water.

VDBP calibrators were made by diluting varying concentrations of Vitamin D Binding Protein (Gc globulin from human plasma, >90% pure, Sigma Aldrich) into a matrix consisting of 125 mM sodium chloride, 25 mM sodium bicarbonate (pH 7.4), and human serum albumin (5% w/v).

Radiolabeled 25-hydroxyvitamin D3 ligand was purchased from Perkin Elmer (Hydroxyvitamin D3, 25-[26,27-3H]—, 5 μCi(185 kBq), Product number: NET349005UC). Radioligand shipped in toluene was dried under a stream of argon and redissolved in acetonitrile. For each binding assay 1 microliter (˜1 nCi) of radioligand was diluted into 100 microliters of binding assay buffer (5% human serum albumin diluted 1:5000 in phosphate buffered saline).

Scintillation counting was performed by mixing all 200 microliters of acetonitrile-extracted adsorbed radioligand or 200 ul of non-adsorbed radioligand into 3 milliliters of Ultima Gold scintillation fluid (Perkin Elmer). Radioactivity was quantified by measuring scintillation decays per minute (DPM) on a Packard TriCarb scintillation counter.

Assay Principal

In this microtiter plate-based competitive binding assay, radiolabeled 25(OH)D3 partitions between VDBP protein adsorbed to the sides of the microtiter plate wells and the VDBP protein within patients' diluted plasma. After binding equilibrium is achieved, the soluble ligand within the reaction buffer is removed and the bound ligand is extracted using acetonitrile. The proportions of ligand that are soluble versus adsorbed are then quantified by scintillation counting. The proportion of adsorbed ligand relative to total ligand is representative of the amount of vitamin D that is bioavailable (i.e. the fraction not bound to patients' VDBP; see FIG. 10). Thus: VRCBA % bioavailable 25(OH)D=adsorbed radiolabel÷[adsorbed radiolabel+non-adsorbed]

In order to relate the proportions of adsorbed vs. soluble radioligand to the concentrations obtained using our calculated bioavailable assay method, purified VDBP (Gc globulin) was used, diluted at various concentrations into a fixed concentration of human serum albumin as a VDBP calibrator solution. Using these calibrator solutions, calibration curves were generated and used these to transform VRCBA % bioavailable 25(OH)D radioligand measurements in patients samples into their corresponding calculated % bioavailable 25(OH)D values (FIG. 11). The absolute concentration of bioavailable 25(OH)D3 in the patient's plasma was then obtained by multiplying the total concentration of 25(OH)D3 by the % bioavailable.

Assay Procedure

Three microliters of patient plasma was diluted into 15 mL of phosphate buffered saline (1:5000). 100 microliters of diluted plasma was added to each well. Plates were chilled on ice in a refrigerated room kept at 4° C. for 15 minutes prior to adding radioligand. 100 microliters of radioligand diluted in binding assay buffer was added to each well and plates were kept refrigerated at 4° C. for 8 hours for binding reaction to reach equilibrium. Soluble radioligand (bound to serum VDBP and albumin from test samples) was separated from adsorbed ligand by pipetting all 200 microliters of the reaction volume from the well without leaving any visible amounts. This fraction was added directly to 3 ml of scintillation fluid. Adsorbed radioligand (bound to purified VDBP and albumin coating microtiter wells) was extracted by adding 200 microliters of acetonitrile. Plate was tipped back and forth to extract any ligand on upper sides of well, and acetonitrile extract was removed and mixed in 3 ml of scintillation fluid. Scintillation vials were, capped, mixed thoroughly, and counted for 2 minutes each. All samples and assay calibrator standards were measured in triplicate. Patient sample measurements were performed in two experiments, Each experiment included measurement of five assay standards containing VDBP calibrators at 1000, 500, 250, 125, and 62.5 micrograms per milliliter. Patient sample measurements of % bioavailable radioligand (defined by the ratio of adsorbed radioligand divided by total radioligand) were converted into their respective calculated % bioavailable 25(OH)D using the calibrator standard curves (FIG. 12). The concentration of bioavailable 25(OH)D (in ng/ml) in patient samples was obtained by multiplying their measured total 25(OH)D concentrations by the calculated % bioavailable 25(OH)D.

Results

Measured and calculated 25-hydroxyvitamin D were correlated (In 13 Gc1S homozygotes: R=0.81, in 33 Gc1F homozygotes: R=0.89, P<0.001 for both, FIGS. 10-12).

Example 7: Measurement of Serum Bioavailable 25-Hydroxyvitamin D Using Immobilized DBP Affinity Extraction

This example describes the measurement of serum bioavailable 25-hydroxyvitamin D using an exemplary immobilized DBP affinity extraction assay. Samples included (1) 5% human albumin mixed with 100 ng/ml 25-hydroxyvitamin D in a Tris binding buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl), (2) The same 5% human albumin spiked with 300 micrograms/mL of purified Gc globulin (Sigma Aldrich), (3) de-identified patient serum containing 60 ng/ml of 25-hydroxyvitamin D, and (4) the same patent's serum spiked with 300 micrograms/mL purified Gc globulin. 100 microliter aliquots of the samples were diluted 1:10 with Tris binding buffer and mixed with 250 microliters of binding resin. The affinity binding resin consisted of Pierce anti-FLAG agarose resin coated with immunoadsorbed FLAG-tagged Gc1S protein. The adsorbed Gc1S protein was produced by transiently transfecting 293T HEK cells with a Gc1S expression vector, and the Gc1S was purified from the cell supernatant by immunoadsorption to the anti-FLAG agarose. After 1:10 dilution, diluted samples were mixed with 250 microliters of resin (coated with 10 micrograms of Gc1S) and incubated at 37 degrees for 15 minutes. The resin was spun down, washed with Tris binding buffer, mixed with isotopic d6-25-hydroxyvitamin D3 internal standard, and the bound 25D and internal standard were extracted with glycine pH 2.5 followed by heptane liquid-liquid extraction. The extracts and calibrators were dried, derivatized with 4-Phenyl-1,2,4-triazole-3,5-dione, and analyzed by LC-MS/MS. 25-hydroxyvitamin D levels were normalized to the added internal standard values to adjust for differences in yield, and absolute amounts of extracted 25-hydroxyvitamin D were calculated based on the calibration curve.

The results, shown in FIG. 15, demonstrated that bioavailable-hydroxyvitamin D may be affinity extracted from serum and detected in this manner, and that the affinity-extractable bioavailable 25-hydroxyvitamin D decreases with increasing concentrations of DBP, as would be predicted. Each reaction was performed in triplicate.

SEQUENCE LISTING SEQ ID NO: 01 Human VDBP Isoform 1, variant 1 NCBI Ref: NP_000574   1 mkrvlvllla vafghalerg rdyeknkvck efshlgkedf tsisivlysr kfpsgtfeqv  61 sqlvkevvsl teaccaegad pdcydtrtsa lsakscesns pfpvhpgtae cctkeglerk 121 lcmaalkhqp qefptyvept ndeiceafrk dpkeyanqfm weystnygqa plsllvsytk 181 sylsmvgscc tsasptvcfl kerlqlkhis llttlsnrvc sqyaaygekk srlsnlikla 241 qkvptadled vlplaeditn ilskccesas edcmakelpe htvklcdnls tknskfedcc 301 qektamdvfv ctyfmpaaql pelpdvelpt nkdvcdpgnt kvmdkytfel srrthlpevf 361 lskvleptlk slgeccdved sttcfnakgp llkkelssfi dkgqelcady sentfteykk 421 klaerlkakl pdatptelak lvnkhsdfas nccsinsppl ycdseidael knil SEQ ID NO: 02 Human VDBP Isoform 1, variant 2 NCBI Ref: NP_001191235   1 mkrvlvllla vafghalerg rdyeknkvck efshlqkedf tslslvlysr kfpsqtfeqv  61 sqlvkevvsl teaccaegad pdcydtrtsa lsakscesns pfpvhpgtae cctkeglerk 121 lcmaalknqp gefptyvept ndeiceafrk dpkeyanqfm wevstnyqqa plsllvsytk 181 sylsmvgscc tsasptvcfl kerlqlkhls llttlsnrvc sqyaaygekk srlsnlikla 241 qkvptadled vlplaeditn ilskccesas edcmakelpe ntvklcdlis tknskfedcc 301 qektamdvfv ctyfmpaaql pelpdvelpt nkdvcdpgnt kvmdkytfel srrthlpevf 361 lekvieptlk slgeccdved sttcfnakqp llkkeissfi dkggeicady sentfteykk 421 klaerlkakl pdatptelak lvnkhsdfas nocsinsppl ycdseidael knil SEQ ID NO: 03 Human VDBP Isoform 2, NCBI Ref: NP_001191236   1 mlwswseerg gaarlsgrkm krvlvlllav afghalergr dyeknkycke fshlgkedft  61 slslvlysrk fpsqtfeqvs qlvkevvslt eaccaegadp dcydtrtsal sakscesnsp 121 fpvbpqtaec ctkeglerkl cmaalkhqpq efptyveptn deiceafrkd pkeyanqfmw 181 eystnygqap lsllvsytks ylsmvascct sasptvcflk erlqlkhlsl lttlsnrves 241 qyaaygekks rlsnliklaq kvptadledv lplaeditni lskccesase dcmakelpeh 301 tvklcdnlst knskfedccq ektamdvfvc tyfmpaaqlp elpdvelptn kdvcdpgntk 361 vmdkytfels rrthlpevfl skyleptlks lgeccdveds ttcfnakgpl lkkelssfid 421 kgqelcadys entfteykkk laerlkaklp datptelakl vnkhsdfasn ccsinspply 481 cdseidaelk nil SEQ ID NO: 04 Human preproalbumin NCBI Ref: NP_000468   1 mkwvtfisll flfssaysrg vfrrdahkse vahrfkdlge enfkalvlia faqylqqcpf  61 edhvklvnev tefaktcvad esaencdksl htlfgdklct vatlretyge madccakqep 121 ernecflqhk ddnpnlprlv rpevdvmcta fhdneetflk kylyeiarrh pyfyapellf 181 fakrykaaft eccqaadkaa cllpkldelr degkassakq rlkcaslqkf gerafkawav 241 arlsqrfpka efaevsklvt dltkvhtecc hqdllecadd radlakyice nqdsissklk 301 eccekpllek shciaevend empadlpsla adfveskdvc knyaeakdvf lgmflyeyar 361 rhpdvsvvll lrlaktyett lekccaaadp hecyakvfde fkplveepqn likqncelfe 421 qlgeykfgna llvrytkkvp qvstptlvev srnlgkvgsk cckhpeakrm pcaedylsvv 481 lnqlcvlhek tpvsdrvtkc cteslvnrrp cfsalevdet yvpkefnaet ftfhadictl 541 sekerqikkq talvelvkhk pkatkeqlka vmddfaafve kcckaddket cfaeegkklv 601 aasqaalql SEQ ID NO: 05 Human proalbumin  rg vfrrdahkse vahrfkdlge enfkalvlia faqylqqcpf edhvklvnev tefaktcvad esaencdksl htlfgdklct vatlretyge madccakqep ernecflqhk ddnpnlprlv rpevdvmcta fhdneetflk kylyeiarrh pyfyapellf fakrykaaft eccqaadkaa cllpkldelr degkassakq rlkcaslgkf gerafkawav arlsqrfpka efaevsklvt dltkvhtecc hgdllecadd radlakyice ngdsissklk eccekpllek shciaevend empadlpsla adfveskdvc knyaeakdvf lgmflyeyar rhpdysvvll lrlaktyett lekccaaadp hecyakvfde fkplveepqn likqncelfe qlgeykfqna llvrytkkvp qvstptlvev srnlgkvgsk cckhpeakrm pcaedylsvv lnqlcvlhek tpvsdrvtkc cteslvnrrp cfsalevdet yvpkefnaet ftfhadictl sekerqikkq talvelvkhk pkatkeqlka vmddfaafve kcckaddket cfaeegkklv aasqaalgl SEQ ID NO: 06 Human albumin dahkse vahrfkdlge enfkalvlia faqylqqcpf edhvklvnev tefaktcvad esaencdksl htlfgdklct vatlretyge madccakqep ernecflqhk ddnpnlprlv rpevdvmcta fhdneetflk kylyeiarrh pyfyapellf fakrykaaft eccqaadkaa cllpkldelr degkassakq rlkcaslqkf gerafkawav arlsqrfpka efaevsklvt dltkvhtecc hgdllecadd radlakyice nqdsissklk eccekpllek shciaevend empadlpsla adfveskdve knyaeakdvf lgmflyeyar rhpdysvvll lrlaktyett lekccaaadp hecyakvfde fkplveepqn likqncelfe qlgeykfqna llvrytkkvp qvstptlvev srnlgkvgsk cckhpeakrm pcaedylsvv lnqlcvlhek tpvsdrvtkc cteslvnrrp cfsalevdet yvpkefnaet ftfhadictl sekerqikkq talvelvkhk pkatkeqlka vmddfaafve kcckaddket cfaeegkklv aasqaalgl SEQUENCE SEQ ID NO: AGCAAAATTGCCTGATGCCACACCCA[A/C]GGAACTGGCAAAGCTGGTTAACAAG 7 GAGCGACTAAAAGCAAAATTGCCTGA[G/T]GCCACACCCACGGAACTGGCAAAGC 8 

What is claimed is:
 1. A method of determining an amount of bioavailable vitamin D in a sample, the method comprising: contacting a sample comprising serum or plasma from a subject with a purified Vitamin D Binding Polypeptide (VDBP) for a time sufficient for free and albumin-bound Vitamin D in the sample to bind to the purified VDBP, thereby forming Vitamin D-VDBP complexes in the sample, wherein the purified VDBP is a fusion protein comprising a peptide immobilization moiety immobilized on a substrate; contacting the sample with a known amount of free labeled Vitamin D, for a time sufficient for the labeled Vitamin D to equilibrate with the Vitamin D-VDBP complexes in the sample; determining an amount of labeled Vitamin D bound to the purified VDBP in the sample; and calculating the amount of bioavailable Vitamin D in the sample from the subject based on the amount of labeled Vitamin D bound to the purified VDBP in the sample.
 2. The method of claim 1, wherein the method comprises removing any Vitamin D not bound to the VDBP from the sample after contacting the sample with the purified VDBP and before contacting the sample with free labeled Vitamin D.
 3. The method of claim 1, wherein the VDBP binds 25-hydroxyvitamin D.
 4. The method of claim 1, wherein the substrate is a bead.
 5. The method of claim 1, wherein the substrate is a magnetic bead.
 6. The method of claim 1, wherein the substrate is a solid surface.
 7. The method of claim 1, wherein the substrate is coated with gold.
 8. The method of claim 1, wherein the substrate is coated with biotin or streptavidin.
 9. The method of claim 1, wherein the substrate is coated with N-hydroxysuccinimide.
 10. The method of claim 1, wherein the substrate is coated with oxirane.
 11. The method of claim 1, wherein the substrate is coated with hydrazine.
 12. The method of claim 1, wherein the substrate is coated with hydroxylamine.
 13. The method of claim 1, wherein the substrate is coated with maleimide.
 14. The method of claim 1, wherein the free labeled Vitamin D is labeled with a radiologically detectable tag; a fluorescent tag; a luminescent tag; or a colorimetric tag.
 15. The method of claim 1, wherein the peptide immobilization moiety is a FLAG-tag.
 16. The method of claim 1, wherein the peptide immobilization moiety is streptavidin.
 17. The method of claim 1, wherein the peptide immobilization moiety is a c-myc-tag.
 18. The method of claim 1, wherein the peptide immobilization moiety is a calmodulin-binding peptide.
 19. The method of claim 1, wherein the peptide immobilization moiety is a polyhistidine-tag.
 20. The method of claim 1, wherein the peptide immobilization moiety is a maltose-binding protein.
 21. A method of determining an amount of bioavailable vitamin D in a sample, the method comprising: contacting a sample comprising serum or plasma from a subject with a purified Vitamin D Binding Polypeptide (VDBP), wherein the purified VDBP is immobilized on a substrate via biotin, N-hydroxysuccinimide, oxirane, hydrazine, hydroxylamine, maleimide, disulfide, vinyl sulfone, or haloacetyl chemistries, for a time sufficient for free and albumin-bound Vitamin D in the sample to bind to the purified VDBP, thereby forming Vitamin D-VDBP complexes in the sample; contacting the sample with a known amount of free labeled Vitamin D, for a time sufficient for the labeled Vitamin D to equilibrate with the Vitamin D-VDBP complexes in the sample; determining an amount of labeled Vitamin D bound to the purified VDBP in the sample; and calculating the amount of bioavailable Vitamin D in the sample from the subject based on the amount of labeled Vitamin D bound to the purified VDBP in the sample.
 22. The method of claim 21, wherein the purified VDBP is immobilized on the substrate via biotin.
 23. The method of claim 21, wherein the purified VDBP is immobilized on the substrate via N-hydroxysuccinimide.
 24. The method of claim 21, wherein the purified VDBP is immobilized on the substrate via oxirane.
 25. The method of claim 21, wherein the purified VDBP is immobilized on the substrate via hydrazine.
 26. The method of claim 21, wherein the purified VDBP is immobilized on the substrate via hydroxylamine.
 27. The method of claim 21, wherein the purified VDBP is immobilized on the substrate via maleimide chemistry.
 28. The method of claim 21, wherein the VDBP is immobilized on the substrate via disulfide chemistry.
 29. The method of claim 21, wherein the VDBP is immobilized on the substrate via vinyl sulfone chemistry.
 30. The method of claim 21, wherein the VDBP is immobilized on the substrate via haloacetyl chemistry.
 31. The method of claim 21, wherein the method comprises removing any Vitamin D not bound to the VDBP from the sample after contacting the sample with the purified VDBP and before contacting the sample with free labeled Vitamin D.
 32. The method of claim 21, wherein the VDBP binds 25-hydroxyvitamin D.
 33. The method of claim 21, wherein the substrate is a bead.
 34. The method of claim 21, wherein the substrate is a magnetic bead.
 35. The method of claim 21, wherein the substrate is a solid surface.
 36. The method of claim 21, wherein the free labeled Vitamin D is labeled with a radiologically detectable tag; a fluorescent tag; a luminescent tag; or a colorimetric tag. 